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User Manual - Hitachi Solutions America

1. Trypsin RRT Use Copy All or Copy Selected Cells from Edit in the menu to copy all or selected cells to the clipboard as tab delimited text Use Save All as or Save Selected as from File in the menu to store all or selected cells in a file as tab delimited text Selecting a Proteolytic Enzyme to Be Displayed 1 Right click the result of analysis in the Sequence View and select the Proteolytic Site List The list of split areas is displayed 2 Click the check box at the leftmost of the list to select any item or items you want to display Uncheck those items you want to hide 3 Click the OK button to complete the setting Chapter 3 Details of Analysis 155 3 36 BLAST Search Amino Acid Types of BLAST Search There are two ways of BLAST search for amino acid sequences Button name Program name Description BLAST search blastp Performs homology search between amino acid sequences and an amino acid database BLAST search tblastn Performs homology search between amino acid sequences and an amino acid database Translation DB translated in all frames One to One BLAST blastp Performs a one to one BLAST search between two amino acid sequences Search Explanation of the Result Window Refer to the Explanation of the Result Screen in Section 19 BLAST Search Selecting a Database to Be Searched 1 Click the BLAST Search icon from analysis button view and an Analysis dia
2. 7 4 6 Switching to Waveform Display Click the Trace View mode button Nh to switch over to the waveform display mode 300 Tutorial La OP borer oe ee ek E ef ants ete Te acate PANTAO GMA S 1 As TET GG Tact GTO a O oy 5 al B 7 4 7 Specifying the Reference Sequence To find the mutation part obtain wild type reference sequences za Click the Import Alignment Sequence button K and specify Tutorial3_2 fsa to obtain the reference sequence For the location of tutorial data refer to 7 1 Before Starting the Tutorial piro Be je CSR A BS OA COF 24a Peer ve P PTH ACCT SERPS T 7 i naaras ec COOK T TOTTI T Te ee Tare Gass TACTIC ACCA CIC AG M SOLS PTS DONT SNESEN IN TTINES IN SF SIIT 676 AT TT EJO T 4OChabGtAT GGT paac VINKI f y br Tocca Teas Tas TAsCT CCATCCCCATCTIEGS we SiN t A fir f 2 PTT GC GOTCATAGTACT TACT PTAA AT CAAA AAdGGCACCATT AD GAAACO Fae eed ees Te a 7 4 8 Alignment with the Reference Sequence Click the Show Alignments button to align the input and reference sequences DNASIS Max uses the Clustal W method to align the two sequences The reference sequence is then displayed aligned with the input sequence and the corresponding waveform data for the input sequence were Because any location having different bases between two sequences is highlighted you can at a glance identify where a mutation has taken place In o
3. 252 Databases 5 8 Codon Table Displays a codon table You can edit the contents of a codon table Codon Table Editor Codon Table Universal x ae Fa a i a R N 4 2 lt G i a 4 on R 4 4 Q 4 D orn R Wl j HE owe 4 ia fl T x fleu z er gt 4 F i gt g 4 Z cl el ra ee flol ls z a ee KNIK OPP gt zj fls 4 2 fa 4 Choose a codon table from the Codon Table list box to display its contents Editing a Codon Table 1 Select the codon table you want to edit 2 Click the z button for the codon to edit 3 Select the corresponding amino acid Select for a stop codon 4 Click the OK button Note User1 to User4 in the Codon Table list are provided for creating a new codon table Chapter 5 Databases 253 5 9 DNA Motif Database You can display a list of DNA motif databases DNASIS MAX supports the functions for creating editing deleting importing and exporting DNA motif databases Window Description Acid Motif Database Manager ofMotifs Modified Comment New SAMPLE fa UserMotifDB1 ser Motif DB2 Iser MotifDB3 312 7 23 295 9 26 This motif database conta Delete 153 9 26 This motif database conta 252 9 26 This motif database conta Basie View Import Export DB Path Item Motif Database list Description Displays a list of DNA m
4. Sa Item Description Plasmid Name Specify the name to show in the center using up to 50 single byte characters Plasmid base length Displays the number of plasmid bases This item cannot be changed Format Selects the display format of plasmid bases Start point Displays the start position of the base sequence This item cannot be changed When tabs other than the Plasmid Tab are selected it is possible to change type and thickness of the line 2 Input necessary information and click OK The plasmid circle will be changed Change Restriction Enzyme It is possible to move or change the size of the restriction enzyme name text area by using the mouse Even when this text area is moved the positions lines that show the links on the circumference of the restriction enzymes won t change Figures can also be changed by changing the restriction enzyme properties The operation is described below 1 Select a restriction enzyme and click on the Toolbar The Plasmid Component dialog will open haerea Coronet xs Resm tr eare l Wwe harten wore nere mna haten eropne poston Item Description Restriction enzyme Name Specify the name for the restriction enzyme up to 15 single byte characters Restriction enzyme position Specify the location of the restriction enzyme in the plasmid bases Minimum value 0 Maximum value Plasmid base length number When tabs other than the Restriction enzyme Tab ar
5. Hyb Oligo DNA Concentration Specifies the annealing probe concentration nM used to calculate the Tm value 190 Details of Parameters Penalty Weights for Hyb Oligo PrimerParametertditor xj General Parameters Primer Picking Conditions PreSequence Inputs Penaty Weights for Primer Hyb Oligo Conditions Penalty Weights for Hyb Oligo Hyb Oligo Tm Lt ji Gt Hyb Diigo Size tt Gt Hyb Oligo GLX Lt 0 Gt Hyb Oligo Sef Complementarity Hyb Oligo N s Hy Oligo Mispriming Hyb Oligo Sequence Quality TAA Item Hyb Oligo Tm Description Specifies penalties for a lower Tm value Lt and a higher Tm value Gt than the optimum Tm value degrees Celsius for the probe Hyb Oligo Size Specifies penalties for a smaller size Lt and a greater size Gt than the optimum probe size bp Hyb Oligo GC Specifies penalties for a lower GC value Lt and a higher GC value Gt than the optimum GC for the probe Hyb Oligo Self Complementarity Specifies a penalty for a higher probe self complementarity than the optimum Hyb Oligo N s Specifies a penalty for a larger number of Ns undefined bases than the optimum within the probe Hyb Oligo Mispriming Currently not supported Hyb Oligo Sequence Quality Specifies a penalty for a lower probe sequence quality than the optimum Chapter 4 Details of Parameters 191 4 11 Oligo Probe Design The parameters for this a
6. The same as selec ing Copy from Edit in the menu The same as selec ing Shape Setting from Edit in the menu SD lds le e 3 The same as selec ing Show Only Checked from View in the menu b The same as selecting Show All Codons from View in the menu rue The same as selecting All Frames from View in the menu s The same as selecting Normal Frames from View in the menu The same as selecting Complementary Frame from View in the menu z The same as selecting Show Comment from View in the menu bad The same as selecting Show DNA Sequence from View in the menu The same as selec ing Show Translation Sequence from View in the menu Chapter 4 4 10 Primer Design General Parameters Penalty Weights for Primer Genera Parameters Pick Up Primer Details of Parameters 185 x Hyd Oligo Conditions Penskty Weights for Hyb Oligo Primer Picking Conditions Pre Sequence bouts D peck left pime F pick right primer F pick hytridestion probe SequercelD Target Erckhded Rapers Product Sew Number To Retuen Max F Stabelity Ma fico o o Mex Fox Max Marine m One Me Hiepmne an Item pick left primer Description Specifies whether to design a left primer 5 upstream primer To design the left primer select the leftmost check box You can also directly enter a sequence to specify the primer You m
7. Click the Chapter 3 Details of Analysis 133 2 In the Clustering Conditions field specify the score and the overlap length Those sequences meeting these similarity standards are classified under the same cluster 3 Click the OK button 134 Details of Analysis 3 29 BLAST Search and Extraction Report This function performs BLAST search for all the DNA sequences displayed in the window takes out those sequences with higher similarity and produces a list containing the results Explanation of the Result Window GridViewer File Edit View Data Help Tj 8 t P frs0997 zl 6 LN A a a EA A e a gt l al Query Datanam Target Dat Sequence Seque Identifier Definition Length Score E val Identiti P 1 x96997 MAM 1261960 gb 9699 7 OASOX2GE O aries SOX 2 gene 3 054 7 903 0 960 2 x96997 MAM 1261960 gb X96997 OASOX2GE O aries SOX 2 gene 3 054 2990 5e 08 151 E x96997 MAM 1261960 gb X96997 OASOX2GE O aries SOX 2 gene 3 054 141 0 3e 03 7 4 Y07510 MAM 407899 gb X 4568 SSPINTIB S scrofa gene for prointerleukin 1 beta 8 760 401 0 02 20 5 Y07510 MAM 1307 gb X62509 0AKD9 O aries KI 9 gene for hair type I kerati 737 342 1 1 6 Y07510 MAM 12018163 gb AF324155 AF32415 Sus scrofa corticosteroid binding globuli 1561 342 1 1 For Help press F1 File menu Export Description Outputs the entire data into a text file Print Preview Displays a print previ
8. The same as the Emphasis selection in the Edit menu Tree View Toolbar zi Explanation The same as the Phylogram selection in the View menu The same as the Slanted cladogram selection in the View menu The same as the Rectangular cladogram selection in the View menu The same as the Unrooted selection in the View menu The same as the Zoom In selection in the View menu The same as the Zoom Out selection in the View menu The same as the Whole indication selection in the View menu Move the phylogram by dragging it Changing the Type of a Phylogenic Tree You can select a phylogenic tree from four types Phylogram Slanted cladogram Rectangular cladogram and Unrooted From the Tree View toolbar select any type you want to display 122 Details of Analysis __ EE 84 690 94 26 Phylogram D EEE EEEN UE I ET E Rectangular cladogram Unrooted Changing the Font 1 Select View Preferences to display the Parameter Set Editor Parameterset Editor Parameterset Name HSKD NASIS Parameterset Type HSK_MultipleAlignmentTreeView3 m Parameters ViewType pooo E ShowBarscale C false true ShowLeaf false true ShowLength false true ShowBootstap false tue DisplayFontName Courier S f DisplayFontSize p o d DisplayFontBold false C true DisplayFontltalic false C true DisplayFontUnderline false C t
9. Database Name TCRTGTNNWNANN alpha_2 CS AATTACCNAATAA Description Displays the name of the database and a list below of all motifs in the database The list shows the name pattern and annotation of each motif Name column Displays the name of the motif Click the column header to sort the motifs by name Pattern column Displays the pattern of the motif Click the column header to sort the motifs by pattern Annotation column Displays the annotation of the motif Click the column header to sort the motifs by annotation New button Creates a new motif This button is disabled if the database is locked Clicking this button makes the Nucleic Acid Motif Property dialog box appear Delete button Deletes the selected motif This button is disabled if the database is locked or if no motif is selected You can also delete more than one motif at one time Property button Allows you to edit the selected motif data Chapter 5 Databases 255 This button is disabled if no motif is selected or if more than one motif is selected Clicking this button makes the Nucleic Acid Motif Property dialog box appear If the database is locked you can browse motif data but cannot edit it OK button Saves the changes made to the motif data and closes the Nucleic Acid Motif Database dialog box This button is disabled if the database is locked Cancel button Discards the changes made
10. Swap Branch Starts the edit command Exchange Branches Emphasis Starts the edit command Set Shading Note At present this function is not available Chapter 3 Details of Analysis 121 View menu Explanation Toolbar Toggles the toolbar to display hide it Status Bar Toggles the status bar to display hide it Phylogram Changes the phylogenic tree display format to Phylogram Slanted cladogram Changes the phylogenic tree display format to Slanted cladogram Rectangular cladogram Changes the phylogenic tree display format to Rectangular cladogram Unrooted Changes the phylogenic tree display format to Unrooted Zoom In Increase the display size Enlarge up to 1000 Zoom Out Decrease the display size Shrink down to 50 Whole indication Display the phylogram according to the window size Preferences Displays a window for setting parameters Help menu Explanation Contents Displays help for the Multiple Alignment Tree Viewer About MultipleAlignmentTree ViewDisplays the version information about the Multiple Alignment Tree Viewer Edit Tree Toolbar Edit tae Explanation The same as the Undo selection in the Edit menu The same as the Copy selection in the Edit menu The same as the Save selection in the Edit menu The same as the OutGroup selection in the Edit menu The same as the Swap Branch selection in the Edit menu
11. This function evaluates the reliability of a tree form using the bootstrap method 1 Click the Phylogenetic Tree icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a Multiple Alignment Parameter Editor will appear ulbipic AlignmentParameterEdtor i x GereratSettines PaimiceAleneert NultipkeAiennent ProteinGep Tree Phykoreti tres C Eniro tee Hunter of bootstrap tiale 1 100900 hoo Seed no 01 1000 att I Evcchache pernitionee with gapa I Corect for multiple miettutions Cancel He 2 Click the Tree tab 3 Select Bootstrap tree Number of bootstrap trials The number of random numbers that occurred Seed No The number of seeds where random numbers occurred Set these parameters 4 Click the OK button 5 Click the Phylogenic Tree button to start analysis 162 Details of Analysis 3 41 Creating Multiple Alignment Profiles Amino Acid Refer to 5 7 Multiple Alignment Profile Refer to Using a Created Profile on Another PC in 3 25 Creating Multiple Alignment Profiles This function creates profiles of multiple alignment The multiple alignment between input sequences is calculated in advance and saved as a profile This allows high speed alignment calculation between an unknown sequence and the profile The Clustal W algorithm developed by J Thompson and T Gibson is used for alignment calculation What is a profile A multiple
12. omeri 4 Click OK Search with the Motif Database Amino Acid 1 Click the Common Motif Search icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button The dialog below appears Analysis Parameter xj Select Parameter Nucleic Acid Motit Search Chapter 3 Details of Analysis 149 2 Select Nucleic Acid Motif Search under Select Parameter then click Set The Amino Acid Motif Search Parameter Set Editor appears 3 Select Use Motif Database then select the database from the list Amino Acid Motif Search Parameterset Edit gt Iv Use Motif Database PROSITE Release 13 Check All Uncheck All Setting 4 Click OK Search by entering the Pattern Amino Acid 1 Click the Common Motif Search icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button The dialog below appears Analysis Parameter Select Parameter Amino Acid Motif Search Collect Motif Results 2 Select Nucleic Acid Motif Search under Select Parameter then click Set The Nucleic Acid Motif Search Parameter Set Editor appears 3 Select Use Input Pattern then input or paste the motif to search m T Use Input Pattern a Help OK Cancel 4 Click OK Setting the Search Method 1 Click the Common Motif Search icon from analysis button view and an Analysis dialog
13. Cuts a portion of a sequence onto the Clipboard Copies a portion of a sequence onto the Clipboard Pa Copies the image of a displayed view onto the Clipboard B Pastes any data from the Clipboard into designated space 6 Window Descriptions For details refer to 1 5 Preferences Dialog Box For details refer to 1 6 Internet Setting Dialog Box Icon Function es Prints the contents of the sequence view pane Print Preview dlo Display the Preferences window Displays the Internet Setting dialog box Displays online help Si B D Displays the Analysis button using a large icon a Displays the Analysis button using a small icon Q Shrinks the Map View Q Expands the Map View Expands any selected area in the Map View Displays the Map View at 100 size Displays a sequence in the Sequence View or the result of analysis on a single line JJ WIS Displays a sequence in the Sequence View or the result of analysis by allowing wrapping according to the width of the window A change in the window size will automatically change the fold back wrapping width accordingly Displays a sequence in the Sequence View or the result of analysis by folding it back according to the number of characters a Lowers the order of a sequence ry Raises the order of a sequence Lowers the order of an analysis Raises the order o
14. 2 Set the Repeat Length and Repeat Count columns 3 Click the OK button Chapter 3 Details of Analysis 109 3 19 BLAST Search This function uses the BLAST algorithm to perform a homology search between a DNA sequence and the specified BLAST database The result of search is displayed in another window Types of BLAST Search There are four types of BLAST search for DNA sequences Button name Program name Description BLAST search blastn Homology search between DNA sequences and a DNA sequence database BLAST search blastx When you enter a DNA sequence performs an all frame translation and then a Protein DB homology search between amino acid sequences and an amino acid sequence database BLAST search tblastx When you enter a DNA sequence performs an all frame translation and then a Translation DB homology search between amino acid sequences and the DNA sequence database that has been translated for all frames One to One BLAST blastn Performs a one to one BLAST search between two DNA sequences Search Explanation of the Result Window The following explains how to operate the menu in the result window F 2 a Menu _ Buton EE Graphic View ie teo 16 B E Alignment View List view File menu Description Export Alignment Exports content in alignment view to a file Export List Exports content in list view to a file
15. 242 Databases Item Description pattern Clicking the Test button causes any section that matches the Test Sequence pattern to be highlighted If more than one section matches only the first match is highlighted This button is disabled if the Motif Pattern or Motif Pattern Test Sequence is not specified It is also disabled if the Motif Pattern Test Sequence contains anything other than alphabetic characters lt button If more than one section matches as a result of a pattern test clicking this button highlights the match previous to the one currently highlighted This button is disabled if the first match is currently highlighted gt button If more than one section matches as a result of a pattern test clicking this button highlights the match following the one currently highlighted This button is disabled if the last match is currently highlighted Motif Annotation Annotation of the motif You cannot edit this item if the database is locked Help button Displays online help OK button If you have opened the dialog box from the Property button the OK button saves the changes made to the motif data and closes the dialog box If you have opened the dialog box from the New button the OK button adds the motif data and closes the dialog box You cannot register a motif having the same name as that of an existing motif You cannot register a motif if its motif pattern is invalid This button is disabled
16. 3 From the Database Selection combo box select a database you want to search through NCBI Advanced BLAST Search NT Program blasin Database fre CAA Program blastp j Database fnr v Option Word size for nucleotide 11 m g u Expect z 0 7 Periodes Filter low complexity Hu Description 100 Alienmamt fioo Query Genetic Codestblastx onb Standard z to ima you BLAST search ro z or enter your organism name here Matr x Gap Existence cost Per residue gap cost Lambda ratio PAM30 9 1 037 PAM70 10 1 0g BLOSUMe2 10 1 og BLOSUME2 11 1 035 default BLOGUMAB 14 2 08 PAMI 2 090 T Output HTML part F Output TEXT part Datat oK Cancel 4 Click the OK button Se Database for DNA sequence search Database for amino acid sequence search Chapter 3 Details of Analysis 157 3 38 Smith Waterman Search Amino Acid This function provides high precision homology search using the Smith Waterman algorithm between the input sequence and the target database and which prevents search misses occurring in the FASTA or BLAST algorithm Types of Smith Waterman Search The Smith Waterman search has two types for an amino acid sequence Button name Description Smith Waterman search Performs a Smith Waterman search between an amino acid sequence and an amino acid sequence database One to One Performs a Smith Waterman search between two different amino acid s
17. FEE RRR N myristoylation site Browsing Details of Searched Common Motifs Click from the Common Motif dialog to display motif details Common Motif Detail List Dialog 01x File Edit Help uj aj gt l Common Motif Detail List CK2_PHOSPHO_SITE PROSITE Release 13 z calmodulin 1 phosphorylase kinase delta Homo sapiens cytochrome c Homo sapiens 152 Details of Analysis Use Copy All or Copy Selected from Edit in the menu to copy all or selected cells to the clipboard as tab delimited text Use Save All as or Save Selected as from File in the menu to store all or selected cells in a file as tab delimited text Chapter 3 Details of Analysis 153 3 35 Proteolytic Site Search This function searches through the amino acid sequence to identify the areas split by the proteolytic enzymes and displays the result of search Explanation of the Result Window aiaiai Ge Ek Soene yow Hb os Be QtO Ff 4 2 4284 2G ttt 2 Oe Dax at CMA Base DNA Seach ONA Company DNA Mipi Sequamnce Armonas Bome Arerokot Seach Map View Sequence View Target calmodulin ohosphoryiase imase deta Momo s Map View A pin shows the identified split area for the proteolytic enzymes If you move the cursor to the pin and click the mouse the display color changes to the selection color indicating the area is selected Sequence View
18. Help Displays online help OK Exits from the Sequence Database Manager Creating a New Database Click New in the DNA Sequence Database Manager screen The New Database dialog box appears A database will be created with the settings specified here You can specify the type of the database that the Sequence Database Manager will create by selecting either the Public or In house tab When the dialog box is opened it displays the Public tab Details follow zes 228 Databases xj ue E Indis Data C GerBark Fist Fie C GenBark tanta Fie Blank Nuckotder r there fwn G Item Description Public Creates a database to store GenBank or other public data data to which a unique ID is assigned In house Creates a database to store in house data such as the experimental data available Public Creates a database to store GenBank or other public data Data you register in this database must have a unique ID assigned Selecting the Public tab in the New Database dialog box displays the following dialog box The DNASpace option is required to update a public database x Nore I intial Date C GenBank Fist Fie GenBank taste Fite Dik Nuckotde O mag mwg e Item Description Name Enter the name of the database Initial Data Select the initial data for the database to be registered GenBank Flat File Read and register data from a GenBank Flat file GenBank FASTA
19. JV 4base cutter JV 5base cutter IV 6base cutter MV Ybase cutter Select from a Category dv Recognition Length 5 Y Cut Kind IV 5 extended IV blunt cut Select from a List User Selected 461 2 MIN 0 The number of cutting sites per enzyme m max 2 we omei Item Description Select from a Category Check to select from a category Recognition Length When selected the restriction enzymes of recognition sequence lengths of 4 5 6 and 7 bp will be selected additionally Cut Kind When selected the restriction enzymes with a cut of 5 extended 3 extended and blunt cut will be selected additionally Select From a List Check to select restriction enzymes from the list User Selected Displays the number of selected restriction enzymes Button Displays the Restriction Enzyme dialog the previous diagram Number of Cutting Sites per Limits the searched restriction enzymes within the upper and lower limits of the frequency of the enzyme cut places MIN Specifies the lower limit of the frequency of the cut places MAX When checked the upper limit of the frequency of the cut places can be specified Help Displays online help OK Saves the set contents and exits the Restriction Site Param Editor dialog Cancel Exits the Restriction Site Param Editor dialog without saving the set contents 194 Details of Paramet
20. Print Setup Display Print Property Dialog Print Preview Display print preview for selected data in the view Print Print the data selected in the view Print All Print all data in the view Exit Closes View Edit menu Description Copy Copies the selected portion of PairwiseView Help menu Description 110 Details of Analysis Contents Displays online help Homology Search Results Displays the version information Viewer Button Description a Toggles the Graphic View to display hide it acer Toggles the Alignment View to display hide it RACAT 5 Toggles the List View to display hide it Display the sequence selected in the view as GenBank Report in the external viewer To display the sequence in GenBank Report Viewer the corresponding Space is needed Print the data selected in the view Display print preview for selected data in the view Graphic View If you click a matched region of the Subject the region is selected and the matched part of the Query is displayed in a color influenced by the Score If you click the white part in the window the selection is canceled By clicking the mouse while pressing the Shift key you can select more than one matching region Explanation of Window Images Query Part Top of the window The numeric value indicated at the top of the bar in the initial status refers to the Query range In the selected status t
21. Sequence ataatatgec cetcttaact actcatenaa tagattgcat tataaaggag ctcacatctc eag Annotation pan i l f a CDS u54801 Sequence totgctgcte tegcgccttc gaagecctet sttetcccce ggagctggcg ctottttegc Annotation source voso Sequence tesatgeaag teagtecaca ttacaggace aactaatcga gagactcatt caacagactc Annotation source CDS CET El A eo Ready I NUM Z Tareet Y07510 Position 1 bp To switch the target sequence click its sequence name or the sequence itself Upper Limit on the Number of Sequences The maximum number of sequences that can be read in a single window is 100 including the number of newly created sequences The value is actually equal to the sum of the numbers of DNA sequences and amino acid sequences 30 DNASIS Basics 2 4 Editing Sequences basic About the Insertion Pointer If you click somewhere on a sequence a vertical bar flashes as shown in the figure at the click point The bar is called the Insertion Pointer Any character entered from the keyboard is inserted at the Insertion Pointer The Insertion Pointer also serves as the starting point for keyboard operations such as the process of deleting sequences Pointer Ways of Moving the Insertion Pointer There are several ways of moving the Insertion Pointer The cursor Up key Moves the pointer to the same position one line above the sequence The cursor Down key Moves the pointer to
22. Show All Annotations Shows all the annotations including the hidden annotations Hide Selected Annotations Hides selected and emphasized annotations including partly selected or emphasized ones Delete Selected Annotations Deletes the selected or highlighted annotation or part Move Up Selected Annotation Moves the selected annotation or part one step forward Move Down Selected AnnotationMoves the selected annotation or part step down Move Selected Annotation To Top Layer Moves the selected annotation or part to the top layer 10 Window Descriptions Move Selected Annotation To Bottom Layer Moves the selected annotation or part to the bottom layer Show Annotation Name and Kind Shows the name and type of annotation Hide Annotation Name and KindHides the name and type of annotation Show Link Opens the URL for the annotation in a browser Rearrange Annotations Restores the annotation modified with Move Up Selected Annotation Move Down Selected Annotation Move Selected Annotation To Top Layer and or Move Selected Annotation To Bottom Layer to the condition at the time of import Chapter 1 1 5 Preferences Dialog Box SS xj Fori Sequence Foking Fuse Sequrce vew Fort Nane fimes Nen Roman Serro fs B Fort Sie REGULAR Line interval Ld Selected Range Pen Cois ME Selected Range Part Coke Emphsen Arca Pen Coe 7 Enphec
23. Window size Corresponds to the window parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter specifies the number of diagonals around the completely matched portion that are used for alignment A smaller value results in higher precision A larger value results in higher speed 210 Details of Parameters Multiple Alignment Make Multiple Aignment Profile Poremeterset Editor Fi xj General PaiwizeAliement WuhipleAlienment ProteivGap Tree Gap Open Penalty 0 100 0 Gap Exteraion Penalty 00 100 Delay divereert gequences 0 100 DNA Transitions Weight 1 0 1 0 Protem DNA fof 6 Protein Weight Matric meres few CY DNA Weigh Matris je J e 7 I Use gegative matrix Item Gap Open Penalty Cancel Help Description Corresponds to the gapopen parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter determines the probability of a gap being inserted A larger value makes it more difficult to insert a gap Gap Extension Penalty Corresponds to the gapext parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter determines the probability of a gap being extended A larger value results in a shorter gap Delay divergent se
24. alignment Corresponds to the quicktree parameter of Clustal W Selecting the check box enables the parameter Note This parameter specifies whether or not to use a high speed algorithm If you select this parameter DNASIS will use the Wilbur amp Lipman algorithm to perform fast approximate processing Without this parameter selected DNASIS will use the Dynamic Programming algorithm to perform relatively slow but accurate processing Protein Chars Specifies the characters permitted within an amino acid sequence that are used to check input data Ifthe sequence contains any character other than those specified here DNASIS does not recognize the sequence as an amino acid sequence This parameter is used only for this application DNA Chars Specifies the characters permitted within DNA sequence that are used to check input data Ifthe sequence contains any character other than those specified here DNASIS does not recognize the sequence as DNA sequence This parameter is used only for this application Default button Returns parameters to default values Chapter 4 Pairwise Alignment Details of Parameters 209 Make Multiple Alignment Profile Parameterset Editor E xj General ParwiseAheniment NuhipleAlienment ProteivGap Tree SLOW Accurate alignments Protem DNA Gap Qen Penalty 0 1000 0 E Gap Exteraion Penalty 00 100 a i Protein Weight Matrec Gore Od EI DNA Weiti Marix fue nT F
25. enzyme data without importing any data Non Enzyme datum window This dialog box appears if the data being imported contains any data other than restriction enzyme data e datum There is non enzyme datum This datum is ignored Skip All Cancel DNASIS cannot import a restriction enzyme which contains this error Check the format of the data you are importing Button Description Skip button Skips the non restriction enzyme data and continues importing subsequent restriction enzyme data Skip All button Continues importing restriction enzyme data skipping all subsequent non restriction enzyme data Cancel button Cancels the importing of restriction enzyme data Clicking this button preserves the original restriction enzyme data without importing any data Registering a New Restriction Enzyme 1 Click the restriction enzyme database button to open the Restriction Enzyme Database Manager a iction Enzyme Date nager New Aarl CACCTGC GCAGGTG 7 not identified Aatl AGGICCT 6 blunt cut Dalai Aatll GACGTC 6 3 extended Aaul TIGTACA 6 5 extended Accl131 AGTIACT 6 blunt cut Acc161 TGCIGCA 6 blunt cut Import Acc361 ACCTGCNNNN NNNN NNNNNNNNGCA 14 S extended Acc651 GIGTACG 6 5 extended Export ccBII GIGYRCC 6 5 extended AccB71 CCANNNNINTGG 11 S extended AccBSI CCGICTC GAGICGG 6 blunt cut Accl GTIMKAG 6 5 extended Acc CGICG 4 blunt cut i i e 2 Click the New button The New E
26. in the figure Enter New Vector Name Type of Vector Circular z Sequence Definition Accession ae Features Features Start End 3 When you create a new vector enter an appropriate vector name in the Enter New Vector Name field an existing vector click Import first to open a dialog box and specify the file you want to import 4 You must fill in the Vector Name Type of Vector and Sequence fields Complete all the settings and then click the OK button 5 The new vector has been added to the Vector Database Manager The cloning site is automatically set the contents and click the OK button Fill in the other fields as required If you use Confirm 82 Details of Analysis Trimming Low Quality End 1 Click the Vector amp Low Quality Trim End icon and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear 2 Set the trimming conditions on the 5 end Place a checkmark in three checkboxes Trim end 5 END and Trim the first P he Oe P g po F mes oe P Tinte tint D ia teose tenn amp Papo r i ae F Sew oe OND P Tom Vector Vectre Nose verte Mere OED Prosete vets ebci yas coneg tte 0 ym mart chome daba chere sie smiet wh OW k Meet com lee ergth conr met er confarnnater te Mermie Matchog Parcmrage coms emet at ostaneet Mier ater Enter a numeric value in the 1 field 10 in
27. s s sssssssssssssssssssstssssstsrsrrssrersrsrersterererersrererererers 89 Changing the Length for a Primer to be Designed 00 0 ieeccceeceeseseeseeecseeecseeseseesceesseescsesaseetseeeeseeaees 90 Exporting the Result to Exel saie A E E RO 90 3 12 OligO Probe Design wise cicsies ccesecsetee ecto ctcdeewectceceeedecaetev ence Da iaaa aaa aaki a 92 Explanation of the Result Window Displaying a List of Probes Exporting the Result to Excel ite 92 Designing Probe ima Specified RESiOM nnsa aeaa e ae AE RE E AAE RA 93 3 13 Restriction Site Search ccccccccsesessscesessceessneesesnensseessseneuennoesnausaseneusnnnesasneuaseesaaooesannonnes 94 Explanation of the Result Window ccsesssesssseseeecseesesecseseescecesesacsecseeasseeaesasaseaeseeassecaesasaeeassaeaceeees 94 Selecting a Restriction Enzyme to be Searched 00 00 ccccececceeseesceecseeeeseeseseeseeecseeecsecaeeessesesseeeseeeaeees 94 Registering a New Restriction ENZYM maai ra cicadas a T E EA E EEE ate ERRE 95 Selecting a Restriction Enzyme to Display sssini EEE EE 96 Selecting a Sequence that Contains a Cut Piece ccc ecceeeseeseseesceecsceecseeecseesesecaeeecsesaeeesseeesseeaesesaeees 96 Looking for a Restriction Enzyme That Cuts Out a Specified Range eee eseeeeseeeeeeeeeeeeeeeeeeeeeee 96 Display Restriction Enzyme Fragment List cece esceeeseeseeeeseeecseeseeeseesecseseesessceesseeecsesaseesseeasseeeees 97 3 14 Motif Seareh ienis eeseciecstadsscd
28. 3054 ISS 3054 oeei 4 To add comments click Add under Comment to display the Add Annotation Comment Dialog Enter the comment key and value then click OK to return to the Annotation Setting dialog 54 DNASIS Basics Add Annotation Comment Dialog Input New Annotation Comment E Cancel 5 Edit in Annotation Setting dialog then click OK to store the modification Deleting Annotation Entries 1 Select an annotation entry you want to delete 2 Right click the annotation entry and select the Delete Annotation menu item 3 This selects the annotation entry Deleting Annotations 1 From the analysis name of column 2 in the Sequence View select an annotation you want to delete 2 Right click the selected analysis name and select Delete Analysis in the menu that appears 3 This deletes the annotation Creating Multiple Annotations You can store annotations after dividing them into groups Suppose for example you want to add CDS information and SNP information as annotations to genome sequences In this case you can create annotations by dividing them into those for CDS information and those for SNP information 1 Select a sequence to which you want to add an annotation 2 Click the _ button on the toolbar to create the first annotation The analysis name for the annotation is called Annotation 3 Similarly click the 2 button on the toolbar to create the second annotation
29. IF Show oigna sequence I Show complementary sequenc Multiple Sequence Calor C ANA Beckgound Foregeound Pertect match F Metchmoethan 51 f r ELA I Colorize Sequerx Bacigound pm Je sd i i Foreground Ireaize Use at Delauls Loja Perfect match Colored when the bases of all sequences match Match more than Colored when the matching rate is higher than a preset value Match less than Colored when the matching rate is lower than a preset value 3 Set the parameters under Multiple Sequence Color 4 Click the OK button Editing an Alignment Sequence You can introduce as well as edit gaps within sequences when they are part of an alignment Use the mark to introduce a gap Changing the Order of Sequences After the initial alignment is displayed you can move sequences up or down in the order to improve the display according to your needs Choosing Sequences in a Project that are to be Aligned 118 Details of Analysis You can use a data list if you want to align only those specified sequences among the sequences displayed in the window 1 On the Switch pane tool bar click the data list button to display the list of sequences in the project BNA AFO11 753 Sequence DNA 46031663 Sequence Cl DNA AFOO9606 Sequence Ci DNA AFOV 751 Sequence Ci DNA AFO11752 Sequence Cl DNA AB016785 Sequence CE DNA AF046866 Seq
30. The Government acknowledges Mirai s representation that the Software is Restricted Computer Software as that term is defined in Clause 52 227 19 a of the Federal Acquisition Regulations FAR The Government acknowledges that the Software is classified as Commercial Computer Software and the Government is acquiring only restricted rights in the Software and its documentation will be as defined in Clause 52 227 19 c 1 and 2 of the FAR Manufacturer is MiraiBio Inc 1201 Harbor Bay Parkway Suite 150 Alameda CA 94502 EXPORT LAW ASSURANCES You acknowledge and agree that the Software is subject to restrictions and controls imposed by the United States Export Administration Act The Act and the regulations thereunder You agree and certify that neither the Software nor any direct product thereof is being or will be acquired shipped transferred or reexported directly or indirectly into any country prohibited by the Act and the regulations thereunder or will be used for any purpose prohibited by the same GENERAL This agreement will be governed by the laws of the State of California except for that body of law dealing with conflicts of law Future updates of the Software will be available for purchase by licensees for a fee provided a registration card has been received by MiraiBio Inc Should you have any questions concerning this Agreement you may contact Mirai at http www miraibio com You acknowledge that you have read this Agre
31. There is non enzyme datum This datum is ignored j Skip All Cancel To skip that non proteolytic enzyme data and continue processing click the Skip button To skip all subsequent non proteolytic enzyme data click the Skip All button To cancel importing data click the Cancel button Recognition site format error If the data in the file specifies a recognition site in an invalid format the dialog box appears To skip that invalid data and continue processing click the Skip button Format Error lt This enzyme have format error You can not import this enzyme i Skip All Cancel To skip all subsequent invalid data click the Skip All button To cancel importing data click the Cancel button DNASIS MAX assumes data to be invalid in the following cases For each sequence separated by a slash 1 There are more than one cut position 2 The data does not have any amino acid characters 3 Any character other than A to Z and is used 4 Brackets are nested in other brackets 5 Brackets are not paired 6 Brackets contain X 7 Brackets contain no characters No enzyme name If the enzyme data in the file does not have a name the dialog box appears To skip that enzyme data and continue processing click the Skip button To skip all subsequent unnamed data click the Skip All button To cancel importing data click the Cancel button No Name Enzyme
32. User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating scores which specify whether DNA matches or does not match Gap Penalty Corresponds to the pairgap parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note When using a high speed algorithm use this parameter to specify the Open and Extension gaps The setting will not affect the processing speed unless you specify an extreme value K tuple word size Corresponds to the ktuple parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter specifies the size of a completely matched sequence A larger value results in faster calculation A smaller value results in higher precision No of top diagonals Corresponds to the topdiags parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note Clustal W calculates the number of complete matches within each diagonal matched position in the sequence and uses the matches having high match ratios for alignment This parameter determines the number n of completely matched positions to be used the n highest match ratios will be used A smaller value results in higher precision A larger value results in higher speed
33. gactat geccceggag ceggecectc etctegtaga cagagcatct cegtgcatca ggcacetast tgagcacaaa actcetettt tectaa aggatt Chapter 2 DNASIS Basics 41 2 7 Editing Sequences advanced Refer to Ways of Selecting a Specific Range in 2 4 Editing Sequences basic Refer to Creating Annotation Entries in 2 11 Annotations Selecting Sequence Ranges You can select a number of non continuous ranges of a sequence at the same time 1 Select the first range 2 While pressing the Ctrl key drag the mouse and select another range 3 These selected ranges are highlighted the first one looks orange the last one looks pink 4 Repeat steps 2 to 3 above caccaaccgc cgcccacagg acgtcaagtt cecgggc ttacctgettg cogcgcagge gcecccaagtt gggtetg ecest Ea ct tzees zzo Getae ty ccce ggcctgggcc ggtaccectg gcecctctat ggcaatg It is also possible to select two overlapping ranges The overlap does not have a special meaning when it comes to usual commands regarding the selected range For annotations however separate annotation entries are created from the viewpoint of the overlap Converting Uppercase and Lowercase Characters You can convert between the uppercase and lowercase characters of sequences Selecting Sequence and then Upper Case or clicking the R button on the toolbar Conversion from lowercase to uppercase characters z Sree 7 Selecting Sequenc
34. more than 10 amp Default Cancel 2 Set the Length and Matching Percentage columns 3 Click the OK button Chapter 3 Details of Analysis 105 3 17 Stacking Site Search Searches and displays the results of stacking site position fora DNA or RNA sequence selected from the sequence editor Explanation of the Result Window Cr a amis ie 1 pema Se bb DU See GABP RRS IN ttt _ erds3aa VVEDEDeGwas a m Map View y a 2 Sequence View a amp i Looe 1 919 ttgg tgasgt cga c Map View Displays stacking areas Click a stacking area to color it as selected and another area as highlighted Sequence View Displays the sequences together with the stacking areas Click a stacking area to color it as selected and another area as highlighted Sequences are selected or highlighted linked areas Displaying a List of Search Results Refer to Displaying a List of Search Results in 3 16 Hairpin Loop Search Setting Parameters 1 Click the Stacking Site Search icon from analysis button view An Analysis dialog box will appear then click the Parameter button and the Stacking Parameterset Editor will appear 106 Details of Analysis Stacking Length 10 bp more than 100 Detour oK _Sancel 2 Set the Stacking Length and Matching Percentage columns 3 Click the OK button Chapter 3 Details of Analysis 107 3 18 Tandem
35. on Cros andl Description Initial setting Specifies the restriction enzyme name using up to 15 single byte characters Item Restriction enzyme name Restriction enzyme position Specifies the position of the restriction enzyme in a plasmid base Specified position Minimum value 1 Maximum value Plasmid base length number When tabs other than the Restriction enzyme Tab are selected it is possible to change the line types and thickness of the drawn line 2 Input necessary information and click OK The restriction enzyme will be added and the restriction enzyme name will appear the first three characters are in italic Inserting DNA 1 Select one or two restriction enzymes of the part to insert and click DMA on the Toolbar The DNA Component dialog will appear However DNA cannot be inserted into areas overlapping with existing DNA or annotations In order to select two enzymes click the second enzyme while pressing the Shift key When two enzymes are selected DNA will be inserted into the one with shorter spacing x OMA jie ja DNA rarae komt stat posho DNA dane longir irant ard potr Drecton Item DNA name Description Initial setting Specifies the DNA name using up to 50 single byte characters Insert start position Specifies the start position of the insertion region Specified position Minimum value 1 Maximum value Plasmid base length
36. Chapter 2 DNASIS Basics 57 2 14 Waveform Display Mode Entering Waveform Files You can display a waveform file also called trace file or chromatogram that the DNA auto sequencer produces The waveform file can be read if its format is ABI or SCF 1 After selecting File and then Open select a waveform file you want to read It is also possible to select more than one file at the same time 2 The sequences stored in the selected waveform file are then read and they are shown in the DNA display mode 3 To display a waveform click the button on the View Toolbar as shown in the figure ioii fe e poro pe He OSB MGE E CE S 82 244 Pits 22 n oo AERE ACCT BB sas GT G CONC G z ganana gt beot Tepi waar hn iio mo In the two row format the bottom row shows the original sequence that has been read from a waveform file In contrast the top row shows a user editable sequence although it is identical to the original sequence under the initial setting See the window below which shows multiple items of data that have been displayed at the same time Since no fold back display takes place you need to scroll through them by means of the horizontal scroll bar Above the base sequence is displayed its sequence name The background for the sequence name is blue which means that it has been selected as the target Therefore it can be executed from the menu or toolbar button You can change targets by clicking somewhe
37. Click the button on the toolbar e Creating Annotation Entries 1 Select a sequence for which you want to create a new annotation entry 2 If there are more than one annotation click the annotation with which you want to associate the annotation entry 3 Click P on the Toolbar The Annotation Setting dialog appears The annotation entry is associated with the annotation you clicked If there was no designated annotation a new annotation is automatically created Annotation Name Annotation Annotation Kind nest Show Link Annotation Range H 1 put annotation range 1 2320 Orient c e C none p Part Range Stan End Add Comment J Key Value Add Line With F 1 Part Width F Color NNT Coor Seti one 4 Enter the Annotation Name and Annotation Kind 5 Enter the value to create an annotation in Annotation Range 6 Specify the direction of annotation entries in the Direction field 7 Click the OK button Assigning Annotation Entries to the Range of Selection 1 Select the range of an appropriate sequence in the Sequence View Chapter 2 Refer to Selecting Ranges in 2 7 Editing Sequences advanced DNASIS Basics 53 2 Click oe on the Toolbar The Annotation Setting dialog appears The value of selected range will be automatically set in Annotation Range 3 Enter the Annotation Name and
38. DNA Search Deleting Analysis Buttons You can delete user duplicated analysis buttons 1 Right click an analysis button you want to delete 2 From the menu select Delete Note that you are only allowed to delete those analysis buttons that you created by duplication not the original ones Changing the Order of Analysis Display You can change the order in which categories of analysis are displayed to provide an easier to read well organized result 1 Click the name of analysis whose order you want to change This will make the analysis name ready to be selected 2 Click the t or button on the toolbar Alternatively you can right click the analysis name in response to a pop up mehi that then appears select Move Up or Move Down 3 Selecting Move Up or Move Down thus changes the order of analysis results Repositioning Analysis Buttons You can change the order of analysis buttons by dragging and dropping a button or buttons 46 DNASIS Basics 2 9 Editing and Analyzing Multiple Sequences Creating New Sequences You can create or add new sequences in a window that displays existing sequences Such new sequences are added at Refer to the end of the list of existing sequences You however can change the order of these sequences Changing the 1 Make sure that the target sequence has not undergone range selection Order of S e 1g 4 Sa eee 2 Select Sequence and then New DNA or click the P butto
39. For the oligo probe design result in sequence view select the sequence name and analysis name then click the Result List Dialog button ioj x Eie Edt _ Help B 5 gt alal ecx 20 55 000 12 Probe i2e4 1303 20 68 997 55 000 2 00 Probe 1631 1650 20 63 983 45 000 3 00 Probe 2707 27268 20 60 008 45 000 3 00 5 Probe 1575 te34 2060 015 60 000 4 00 eet Exporting the Result to Excel 1 For the primer design result in sequence view select the sequence name and analysis name then click the Result List Dialog button 2 To copy the whole list into Excel simply save as text file and open the file in Excel Chapter 3 Details of Analysis 93 3 Alternatively Select Copy All or Copy Selected Cells from Edit in the menu Copy All Copies all the information being displayed Copy Selected Copies only the columns that have been selected Paste the copy to an MS Excel sheet Designing a Probe in a Specified Region 1 Click the Oligo Probe Design icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button 2 On the Pre Sequence Inputs page enter an appropriate value in the Included Region field Use the following format lt start bp gt length In the example the design is based on a length up to 149bp from 50bp to 100bp PrimerParameterEditor x Penalty Weights for Primer Hyb Oligo
40. Opt The primers whose length is as close to this value as possible are designed Max The maximum length for the primer to be designed Note The primers whose length is longer than this value cannot be designed 4 Click the OK button Exporting the Result to Excel 1 For the primer design result in sequence view select the sequence name and analysis name then click the Result List Dialog button 2 To copy the whole list into Excel simply save as text file and open the file in Excel 3 Alternatively Select Copy All or Copy Selected Cells from Edit in the menu Copy All Copies all the information being displayed Copy Selected Copies only the columns that have been selected 4 Paste the copy to an MS Excel sheet Chapter 3 Details of Analysis 91 Rew ius ed o a EA a boll e bd bid a a ESS 8835 Got Ess ue Uus Nuu Hax 92 Details of Analysis 3 12 Oligo Probe Design This function designs oligo probe for DNA sequences Explanation of the Result Window 7 Untitled DNASIS aloj xj Ge G Sequence Yew tap Ose hae 68 4188 Bane a2 04442 e wl AH Da G tela EA TE Map View Sequins Gin Bast D Sequence View Sequeres aim Paa D The designed probe is displayed on the bar You can change the number of probes that you want to display If you click the probe portion the corresponding sequence is selected Displaying a List of Probes
41. Setting an QuieGroup ia NE dead aves tae canta recs wendeeeas tebe avaascenssearervaesceon venereum netuenonens Exchanging Branch es nn Ean e ue crden E EE OS E E RRE Evaluating the Branching Reliability Bootstrap Tree cceceeceeseeseeseeeeeeseeeeeseeseeseeseeseceeeeeeeeeaeeneeneees 123 3 24 Create a Phylogenic Tree for Manually Edited Alignment ccssscseseeeeeeseeneeeeeees 125 Proced ra n aa aee A E AERE EE EE EE E A O E E E 125 Result Window Description s ssi scissscstsscsscessibeesscesccessedsicayasssccendedadeayacateceisedadedsassnaceysedadedssssnaseysndadeasssiaaie 125 3 25 Creating Multiple Alignment Profiles ccccccesseeeeeeeeeeeeeeneeeeeeeneeseeeseenseeeseeseeeeseenseenenes 126 Procedure for Creating a Profile cece 126 Using a Created Profile on Another PC 127 3 26 Using Phylogenic Trees Profiles DNA ccccessscssseereeseseeneeeesneeeeseeeeeseeeseeeseeeseeneeeeeees 129 Analysis Proc d ren iana eraen vax casas tees AA a seven casas aback cub E e share iviahoneus Stara S 129 Explanation of the Result Window sisssiissccssiscsascasscesesssstaxseassceneassicassessdcessnasddansessdasdessseceacassdvesanasieaassineie 129 3 27 SEQUENCE ASSOMDIY raisen naaraana ERIAN cenduecd esuiece dusted cdeesdiceecasseredeesiiececeseas 130 Explanation of the Result Window cescsscssseseessceseeseeseeseesecseceeceeceaeesecaecseceeeeaecaeeaeeaecaeeeeeeeeeaeeaeeneens 130 Setting Parameters uio E
42. Specifies the account name of the receiving mail server Specifies the password of the receiving mail server Chapter 1 1 7 Data List Window Window Descriptions 15 Item Description Type Displays the type of a sequence Data Name Displays the sequence name Analysis Name Displays the analysis name Seq Sets the display condition of the Sequence View Ext Indicates that there is another window indicating the result Show Checks the Seq field for selected analysis Hide Unchecks the Seq field for selected analysis Open Opens the result shown in another window Delete Deletes specified analysis Select All Selects all the lists currently being displayed Deselect All Cancels all the lists currently being displayed 16 Window Descriptions 1 8 Analysis Dialog x Icon Trimming Comment Comment Raw data from sequencers often contain irelevant sequences such as vector sequences at the 5 and 3 ends Conducting homology search with sequence data containing such irrelevant sequences low quality sequences will greatly decrease the accuracy of the searches T Execute analysis without showing this dialog Parameter Parameter button Execute button Show Dialog Checkbox Item Description Icon Shows the analysis button that was selected Comment Shows the content of the analysis button that was selected Show Dialog Checkbox If checked
43. There is no name enzyme You can not import no name enzyme j Skip All Cancel Duplicate enzyme name If the enzyme data in the file has a name which is used for another existing enzyme the dialog box appears Chapter 5 Databases 261 This enzyme is already registered Please select skip or overwrite SkipAll Overwrite Overwrite Al Cancel To skip that enzyme data and continue processing click the Skip button To skip all subsequent duplicate named data click the Skip All button To overwrite the existing enzyme data with the imported data click the Overwrite button To overwrite all subsequent duplicate named enzyme data with the imported data click the Overwrite All button To cancel importing data click the Cancel button Exporting Proteolytic Enzyme Data In the main window you can click the Export button to export data for the proteolytic enzyme Clicking the Export button causes the following dialog box to appear Select the name of the file to which you want to export data in this dialog box and export data tia Save in a Too Jee Oc G Fi neme Pateda r repre penare Save Sava aipe Preap Enges Fies peranci S Canal Errors that may occur when exporting data Too long enzyme name If the name of the proteolytic enzyme exceeds 255 characters the following dialog box appears e Database Manager dbtool HitachiSoftware Engineering HitachiSoftw
44. This parameter is used only for this application DNA Chars Specifies the characters permitted within DNA sequence that are used to check input data Ifthe sequence contains any character other than those specified here DNASIS MAX does not recognize the sequence as DNA sequence This parameter is used only for this application Select create datas Select Do Multiple Alignment only For a phylogenic tree select Do Tree only or Do Multiple Alignment and Tree Default button Returns parameters to default values Chapter 4 Pairwise Alignment Details of Parameters 203 MultipleAlgonmentPorameteridtor i 18 x GeneralSettings PairmizeAlienmers MultipleAlienment ProteinGep Tree SLOW Accurate alignments Protem DNA Gap Qen Penalty 90 1000 i E Gap Exteraion Penalty 00 100 a i Protein Weight Matrec Gore Od EI DNA Weiti Marix fue nT F FAST Approximate alignments Protem DNA Gap Peewlty 0 500 j E K tuple word size Froteini 2 DWAT 4 gt EEE me No of top diagonalt 1 50 m TEE Widow see 0 50 TE E Item Gap Open Penalty Carcel Help Description Corresponds to the pwgapopen parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Gap Extension Penalty Note This parameter determines the probability of a gap being inserted A larger value makes it more difficult to insert a gap Corres
45. Waveform Display os rnnr seneneoenn i aaeeea ASEA ENERE EVEEN AAEE KEERAS NEK REO 299 7 4 7 Specifying the Reference Sequence 300 VAS Alignment with the Referenc Sequences ys 0csaiscesiseeciaeeds E R E EN NN 300 gt apse en i D E P re OES l a Preface xiii Preface DNASIS MAX v2 5 USER S MANUAL Published by Hitachi Software Engineering Co Ltd Address Hitachi Software Engineering Co Ltd Life Science Research Center 1 1 43 Suehiro cho Tsurumi ku Yokohama 230 0045 Japan First Edition November 2001 invalid Second Edition February 2003 invalid Third Edition November 2003 invalid Fourth Edition March 2004 November 2001 Hitachi Software Engineering Co Ltd All rights reserved This book contains the proprietary information of Hitachi Software Engineering Co Ltd No part of this document including design cover design and icons may be reproduced or transmitted in any form by any means electronic photocopying recording or otherwise without prior written agreement from Hitachi Software Engineering Co Ltd The software described in this document is furnished under a license agreement Hitachi Software Engineering Co Ltd Retains all ownership rights to the software programs and related documents Use of the software and related documents is governed by the license agreement accompanying the software and applicable copyright law DNASIS is a registered trademark of Hitachi Softwa
46. amino acid sequence If this parameter is set to DNA inputting amino acid sequence data as determined by DNASIS MAX results in an error and the sequence is not processed Output Order Corresponds to the outorder parameter of Clustal W You can select either Order by Aligned or Order by Input with which the value aligned or input will be set respectively This parameter specifies the order of the input sequence data within the result output from Clustal W Ifyou select Order by Aligned DNASIS will output the results arranged in the order in which they appear in the guide tree or phylogenic tree If you select Order by Input DNASIS will output the results arranged in the order of the name of the input sequence data Use FAST Algorithm for the alignment Corresponds to the quicktree parameter of Clustal W Selecting the check box enables the parameter Note This parameter specifies whether or not to use a high speed algorithm If you select this parameter DNASIS will use the Wilbur amp Lipman algorithm to perform fast approximate processing Without this parameter selected DNASIS will use the Dynamic Programming algorithm to perform relatively slow but more accurate processing Protein Chars Specifies the characters permitted within an input amino acid sequence If the sequence contains any character other than those specified here DNASIS does not recognize the sequence as an amino acid sequence
47. e Sequence masking e Alignment with the reference sequence 7 4 1 Starting DNASIS MAX Refer to Starting DNASIS MAX in 7 2 ORF Search 7 4 2 Using the Editor to Open Sequence Files The Tutorial uses Tutoria3_1 abi as its input sequence From the Sequence Editor s File menu select Open and specify Tutoria3_1 abi For the location of the tutorial data refer to 7 1 Before Starting the Tutorial 7 4 3 Registering Vector Sequences with the Vector Database Select the Database on the analysis button bar pe Register to In house OB fONA4 a am Sequence Database ia Blast Database G NCBI Entrez Search 1 4 Vector Database S AminoAcid Mott Database me Restiction Enzyme Database Clicking the Database button K displays the vector database manager window Cloning Site Features Features 43 244 promoter 280 4932 firefly luciferase 303 281 GLprimer2 sequencing primer binding 1964 2185 V40 late poly A signal 227 2053 RVprimerd sequencing primer binding aio 2510 ColE 1 derived plasmid replication orig 4132 13272 heta lantamase Edit Add Delete Edit Add Delete a ggtaccgagc tcttacacet gctagcccag actcgagatc tecgatctec atctcaatta gtcagcaace atagtcccgc ccctaactce gcccatcccg ccectaacte cacccagttc cacecattct ccgccccatc gctgactaat tttttttatt tatecagags ccgaggccec ctcgecctct gagctattcc agaastasts ageagacttt ttteeagacc tagectttte
48. e e Poe Ps ser Bene SSCS Tt tw fmeonne SSCSCSC C e Asx Psparagineandasparicacd 2 Gk etutamine and gktamic acid Stop codon This is displayed at the time of translation a rom DNA however it cannot be entered PX ex Yndeterminate aminoacid e Pe a The input process is case sensitive uppercase and lowercase characters are distinguished However the analysis process is not case sensitive users are allowed to assign their own meanings to uppercase and lowercase characters Chapter 2 DNASIS Basics 23 Entering and Editing Multiple Sequences You can edit multiple sequences in a single project window With a DNA sequence already displayed select Sequence and then New DNA alternatively you can click the A button on the toolbar The new sequence is then added below the existing sequences To switch the sequence being edited click the target sequence The same procedure applies to amino acid sequences 7 meted ONASIS te tH gt oma er tee oe ee QA 4B aR 2 0 t24 eye BSS D s Gw ast i vy DNA Beer rem nem Switching between DNA Sequences and Amino Acid Sequences for Display DNASIS lets you enter both DNA sequences and amino acid sequences into a single project although they cannot be displayed in the Sequence view pane at the same time It is necessary to switch between DNA sequences and amino acid sequences for display To switch to the mode of importing or enter
49. 0 Penalty foe Primer Pars Product Sze Lt 005 Gt 0 05 Product Tm Lt f0 Gt Tm Diterence Ary Complementanty 3 Complemertanty Por Maprenng Primes Penalty Weaght 1 Hyd Oligo Penalty Item Penalty for Primers Description Tm Specifies penalties for a lower Tm value Lt and a higher Tm value Gt than the optimum Tm value for the designed primer Size Specifies penalties for a smaller length Lt and a greater length Gt than the optimum length of the designed primer GC Specifies penalties for a smaller GC Lt and a greater GC Gt than the optimum GC for the designed primer Self Complementarity Specifies a penalty for a larger self complementarity than the optimum N s Specifies a penalty for a greater number of Ns than the optimum Mispriming Currently not supported Sequence Quality Specifies a penalty for a lower sequence quality than the optimum End Sequence Quality Specifies a penalty for a lower quality than the optimum at the 3 end of the primer 3 Self Complementarity Specifies a penalty for a higher self complementarity than the optimum at the 3 end of the primer Position Penalty Specifies a general penalty relating to the primer position End Stability Penalty for Primer Pairs Product Size Specifies a penalty for a lower stability than the optimum at the 3 end of the primer Specifies penalties for a smaller size Lt and a gre
50. 0 wot J t DB Path Item Description a This icon indicates that the database stores DNA sequence data GenBank or FASTA files provided by NCBI Da This icon indicates that the database stores amino acid sequence data GenBank or FASTA files provided by NCBI Fi This icon indicates that the database stores in house DNA sequence data such as the experimental data available fs This icon indicates that the database stores in house amino acid sequence data such as the experimental data available Name Displays the name of the database of Seqs Displays the number of sequence data items stored in the database Date Displays the date on which the database was updated last Comment Displays comments if any New Creates a new database Clicking this button displays the New Database dialog box Property Displays information about the selected database View Shows the entries registered in the selected databases Refresh Updates the database list with the latest information Delete Deletes the selected database Empty Deletes all entries from the selected database You can use this button for example if you have inadvertently registered a large number of sequences in an in house database Daily Update Not supported in this version DB Path Allows you to set the path of the directory to store the database Usually you do not need to modify the path
51. 1000 Gap Exteraion Penalty 00 100 Delay divereert gequences 0 100 DNA Transitions Weieht 1 0 1 0 Protem DNA oy S Protein Weight Matric meres few CY DNA Weigh Matris je J e 7 I Use gegative matrix Item Gap Open Penalty Cancel Help Description Corresponds to the gapopen parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter determines the probability of a gap being inserted A larger value makes it more difficult to insert a gap Gap Extension Penalty Corresponds to the gapext parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter determines the probability of a gap being extended A larger value results in a shorter gap Delay divergent sequences Corresponds to the maxdiv parameter of Clustal W Note This parameter prevents DNASIS from aligning sequences having distant relationships until it aligns the sequences having the closest relationship DNA Transitions Weight Corresponds to the transweight parameter of Clustal W Note This parameter specifies a value of 0 or 1 for replacement If 0 is specified DNASIS does not assume replacement as a match If 1 is specified DNASIS assumes replacement as a match You should specify 0 for closely related DNA sequence data and 1 for distantly related DNA sequenc
52. 289 fien rean eee D ooe pome pe De BEA DOP 2498 4 2 44 235 22 se s3ea ee b ees DeOw as OW Bem a o ia amp oj 5 Tog Tandin iS aae iie 7 2 5 Displaying Only the Longest ORF If there are too many ORFs to be read with ease you can reduce the number of ORFs that are displayed at the same time Right click your mouse on the displayed ORF results and select the Show Settings menu Frame I Frame 1 W Frame 1 I All Frame I Frame 2 I Frame 2 I Frame 3 Frame 3 7 ORFs in kneth I Minimum Leneth T bp Other I Nested ORF Show Comment Show FrameNo ee ee Place a checkmark for Show Top Number ORFs in length in the ORF field and fill in it with an appropriate number When we select a number n here only the n longest ORFs will be displayed In our example we ll select 1 because we want to display only the longest ORF If You Want to Display the ORF List In sequence view select the sequence name and analysis name then click the Result List Dialog button If you want to store the ORF list click the Save All button This allows the information displayed in MINJ ATOTACAAOATOATOOA MONS ATOATORAIACGGAD MEME ATOGAGACGGAGCTOA IEn ATGAROGOCTTOATGST mane AToOTETGSGTOCOGOGS Mom ATOOOOOAADADAATC ITS ATOCACAACTOGOAGA ZMES ATOANIIAGC ADDR TET IS ATGAAGAAGGATAAGT W ATaGOGAGOGESS TOS IMSI ATODAOAOCTAOOOOK WNE ATOAROOOCTOOANDA 15W05
53. 3 The exclamation mark indicates the position to cut If the recognition sequence does not have a palindrome structure the sequence recognized by a Normal sequence and that recognized by a Complementary sequence are separated with a slash Bases Indicates the number of bases in the recognition sequence Kind Of Cut Indicates the shape of the cut performed by the restriction enzyme 5 extended Cuts the sequence so that the 5 end is longer than the 3 end 3 extended Cuts the sequence so that the 3 end is longer than the 5 end 5 GAATTC 3 ae blunt cut Cuts the sequence so that the 3 and 5 ends have the same length not identified ees 3 ACGCGT 5 Indicates that you cannot identify the position to cut for this restriction 5 CCQGGG 3 3 ACGCGT 5 enzyme If you check this enzyme it will not be registered as a parameter Restriction Enzyme Database Manager button Starts the Restriction Enzyme Database Manager HTML Mode Select this check box for DNASIS Restriction Codon Table Specifies a codon table to be used 196 Details of Parameters 4 15 Hairpin Loop Search Length Stem j 7 Gp lop 4 7 p Matching Percantage more than 10 Default Cancel Item Description Stem Length Specifies the stem length If the stem length is within the range specified here the stem length will become a hairpin loop region candidate Input range 2 to 99 Loop
54. 33 Motif Search AMINO ACid ccccccste seston seceeeseesesneeseeeeeseceaessaeseseeeseseeesseaescaeseeneeseneenas 143 Explanation of the Result Wind Owes odssssectcestesstdccsveancdecat a rade erenater E E ESE 143 Search Using a Motif Databases ss vic seeleantie at oi aa E E eae sence ed deere lan 143 Search by Entering a Motif Pattern issons n E sey ssaacdevesanesenanasetave GEE 144 Creating a Motif Database ia cccecsnececcesssuesssessvesetapenecoubesnecestpenecusnseeecouseroceessanenevepvencenepeuveutaueeresseueecconge 144 Contents ix Adding Mott Datars cert i a eroi a A oveceddovans EAE E E A E R 145 Browsing the Detail of a Motif Searched for s sssssssssesesrsssssssssssssssstststsestentseneneneneeerrtsrsrstsesrsrsrerrs 145 Displayinga Listo Search Results sese aes EERE EEE EEA R ERRE 146 3 34 Common Motif Search rasonas ninte arrenar serora reana i pinne k ansarap kesa non kbp i sans Sannaa pni pnra pksa naat 147 Result Window Description wa 147 Search with the Motif Database DNA we 147 Search by entering the Motif Pattern DNA deesses tea r eiai EE AEE ERSE E 48 Search with the Motif Database Amino Acid cee eeesecseeeceeseseeseeecseeecsecaeeecsecaesesseeesseesesesasees 48 Search by entering the Pattern Amino ACid eee eceecseeeeeeeseeescesesecsceecsesaceecsecaesesseeesseeseseeasees 49 Setting the Search Methodi nisinge ieis eiin E AE EE E EE ETE 49 List up Search
55. 40 Stem Area Stem Area Loop Area Map View Displays total hairpin loop areas Click a stem area to color it as selected and another stem area as highlighted Click a loop area to color the total hairpin loop area as selected Sequence View Displays the sequences together with the stem loop areas Click a stem area to color it as selected and another stem area as highlighted Click a loop area to color the total hairpin loop area as selected Sequences are selected or highlighted linked areas Displaying a List of Search Results For analysis result in sequence view select the sequence name and hairpin loop name then click the Result List Dialog button 104 Details of Analysis hs rotator Ot eee 2151 x Eile Edit Heb By Bro Se 4x allal Nome Kr Comment B Harpnbop 100 08 24 B Hairpnboop 100 08 50 63 B Harpnbopi 100 0 168 182 B Harpnbopt 100 0 193 204 E HorpnioopS 1000 213 224 4 F Dram annotation name and kind LCa Cancel j In the dialog the list of hairpin loop areas can be copied saved printed and so on For detail refer to Annotation List Dialog in 4 32 Annotation Setting Parameters 1 Click the Hairpin Loop Search icon from analysis button view An Analysis dialog box will appear then click the Parameter button and the Hairpin Loop Parameterset Editor will appear Hairpin Loop Search Length Stem 7 p Loop 4 7 p Matching Percentage
56. 4FE4S_FERREDOXIN PATTER 5_NUCLEOTIDASE_1 PATTERI 5_NUCLEOTIDASE 2 PATTERI 6PGD PATTERN nACG PS00 A4_EXTRA PATTERN nAG Ad INTRA PATTERN nAC F A DFAMINASF PATERNO Help You can create edit or delete amino acid motif data Item Database Name Description Displays the name of the database Motif data list A list of all motifs in the database The list shows the name pattern and annotation of each motif Name column Displays the name of the motif Click the column header to sort the motifs by name Pattern column Displays the pattern of the motif Click the column header to sort the motifs by pattern Annotation column Displays the annotation of the motif Click the column header to sort the motifs by annotation New button Creates a new motif This button is disabled if the database is locked Clicking this button makes the Amino Acid Motif Property dialog box appear Delete button Deletes the selected motif This button is disabled if the database is locked or no motif is Chapter 5 Databases 241 Item Description selected You can also delete more than one motif at one time Property button Allows you to edit the selected motif data This button is disabled if no motif is selected or if more than one motif is selected Clicking this button makes the Amino Acid Motif Property dialog box appear If the database is locked you can browse the motif data but canno
57. 56 Opening Projects cscs sctssestescsssssscessschiesesssssaczestascessssdsizasttescesgtadstesstaancsesseeueg sae VUNE EEEE Ee SRIEP IRE SaS 56 2 14 Waveform Display Mode ccceccccesseneeesseeeeeesneneeeeseeeseseseeseseseaeseseneaeseseseeseeseseaeseseseanseeesnes 57 E t ring Waveform Files i s ses sbacceassccssdensidesacvatedsdecsicsaecaiaaseesshiasatssdoascecshiesacshied SEET EPSE SEa SiE EEPE aSa 57 Switching between Waveform and Sequence Displays s sesssssseseierererersrsrsrerssssesssrsrsrnrnrernrerererererenee 58 Selecting Waveforms to Be Displayed sierici iiei e EE E A 58 Displaying Reverse Complement Sequences 58 Editing Sequences While Viewing Their Waveforms 58 Returning to the Original Condition when Editing 58 Hiding Specific Lanes soye E E Mee nena ne ane aaa nen sone tne acme 59 Expanding and Shrinking Displayed Waveforms 0 00 0 cccecceescesesseseeeeseeecseeeceeeseesseesesesaceecaeeassesaeetaees 59 Changing the Coloriof Waveforms sa ogon r n eE ea deans EEEE RE E O 59 Making Alignments with Reference Sequences s ssssssssssesesesssesstessreserrtrtrtstststsrsrsrsrsrnrsrsrerersrrerersres 59 Scrolling through Multiple Waveforms Horizontally and Separately ccccesesceseeeeeeeeeeeeseeseeeeeeneees 59 Copying Trace Data si pinoa ann a nvecn sissies wien Ass tetaer sate aueete es de eee Gen eer tener anaes 60 2 15 Saving Sequences as Text Fil S ccccsseccceeseeeeeseeeeeeeeeeeeeeeseeeseseseee
58. 6 Brackets contain X 7 Brackets contain no characters Comment Displays comments for the proteolytic enzyme if any Button Description OK button Registers the proteolytic enzyme with the entered data DNASIS MAX cannot register an enzyme if its modified name is already used for an existing enzyme In sucha case you must change the name to register it Cancel button Cancels the editing of new proteolytic enzyme data Errors that may occur when editing data Duplicate enzyme name For renaming an enzyme that is already registered the dialog box appears Protec ager dbtool E3 1 Chymosin is already registered fs 5 Please change enzyme name Click the OK button to return to the Enzyme Property dialog box Change the name of the enzyme and retry Importing Proteolytic Enzyme Data In the main window you can click the Import button to import data for a proteolytic enzyme Clicking the Import button causes the following dialog box to appear Select the file to import in this dialog box and import data 260 Databases aix Look in a Toot Je 00m m ProteciytcEneyies penrre Fie rame Provechact nawres penze Fies of type P teok Enzyme Files penzyme gt Corcel Errors that may occur when importing data Non proteolytic enzyme data If any data in the file is not proteolytic enzyme data the dialog box appears Non Enzyme datum
59. 8 1 5 Preferences Dialog BOX wiiiic ccciicic ccc ceicciee cesietee kananan nn naaa anann reseenen ceeeetee seston seevetee es 11 1 6 Internet Setting Dialog BOX rrsan rnronnneann anne anaana Rna ne REAA AANA nA An PARATE BARNEN NRR RA SANANA RAAN MARENE S 13 1 7 Data List Witt OW iein a a aaa a a a aa das a a a aa aE a aa aa aaa a a leeds 15 1 8 Analysis Dialogs ou cisicc ccccecciececice tess chet cvceteed evecdteeeectttcesescebed eveeuted ENa AEKA P ANNAN E Eaa N RATAAN EN NAARAS 16 Chapter 2 DNASIS Basics sciccscscansicexececcccsscecasexeivccccxecacccscacesacensencsecsaansedexscenecatrceenae dL DA Start liGs DNASE E E A N cota aed 18 Importing Sequences from a Sequence Database eieeeesecseeseseeeeseeseecseeecseeseseeseeesseeecsesaeeesseeeeaees 18 Showing Entries ees wed NN teal ale OEO E eevee Sian E A EN ends lend aiid Ale 19 Obtain sequences from NCBI Eitrez 29 s5 ssesess bsnsesscadstcassianceaysudstes sesveraysetadsasseasacesssoasass aa si ssesetestecd a seas 20 2 2 Entering SQQUCICES icccciesiscccientceediesiceeceentcevitestenecdentceedeendueedeendcendtesderecdentdeedtesdurecsentonedtentey 21 Creating DNA Sequences da anc ssSeuicciess idasAhsh lash sShsazausesbeces ase ideesste ides shactsadstacdvesanstecavstsicese Characters You Can Use for DNA Sequences ccccceccesescescseeseeeeseeecseeseeecaeeecsecaeseesesesaeeecsesaeeesseeaeaee E tering Amino Acid Sequences 3 i 08 eee ean entity E tes ea Characters You Can Us
60. Add citation 1 codon start 1 wast db xref GI604479 Eoen gene DP2 product DP2 ca protein_id AAB60378 1 translation MISTPQRLTSSGSYLIGSPYTPAPAMVTQTHIAEAT Line Width 321 Part Width Color NNN Color Setting Cancel Item Annotation Name Description Shows the annotation name Annotation Kind Shows the annotation type Link URL Shows the annotation URL link Show Link Displays the webpage of the Link URL Annotation Range Shows the annotation range Orient Selects the annotation orientation Part Range Shows the annotation part range Start Shows the annotation start position End Shows the annotation end position Add Displays the Add Annotation Part dialog to specify the part range Delete Deletes the selected Part Edit Edits the selected Part Comment Shows annotation comments Key Shows comment keys Value Shows comment values Add Displays the Add Annotation Comment dialog Adds comments in the Add Annotation Comment dialog Delete Deletes the selected comment Edit Edits the selected comment Line Width Shows the line width Part Width Shows the line width horizontal of Part Color Shows the annotation color Color Setting Sets the annotation color OK Sets the selected contents as parameters and exits from the Annotation Setting dialog Cancel Exits from the Annotation Setting dialog wi
61. Align the cursor to the pin and click to color and highlight it as selected Sequence View Displays the sequence together with the common motif name and recognized parts Click the motif name to color and highlight it as selected Search with the Motif Database DNA 1 Click the Common Motif Search icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button The dialog below appears Analysis Parameter xj Select Parameter Nucleic Acid Motit Search Collect Motif Results Close 2 Select the Nucleic Acid Motif Search under Select Parameter then click Set The Nucleic Acid Motif Search Parameter Set Editor appears 148 Details of Analysis 3 Select Use Motif Database then select the database from the list IVISAMPLE Check All Uncheck amp ll Setting 4 Click OK Search by entering the Motif Pattern DNA 1 Click the Common Motif Search icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button The dialog below appears Analysis Parameter xj Select Parameter Nucleic Acid Motit Search Collect Motif Results coe 2 Select Nucleic Acid Motif Search under Select Parameter then click Set The Nucleic Acid Motif Search Parameter Set Editor appears 3 Select Use Input Pattern then enter or paste the motif to search Use Input Pattern uywaTowy
62. Analysis Buttons spees es sects coves ccqeessundcessbades satabsiasstecdeusssadseuessauiegauauecuenieudaaenatieetan iets 45 2 9 Editing and Analyzing Multiple Sequences cccccessseeeeeseeneeeeseeeeeeeeseeeeeneeeneeeeseneeeeeeseenens 46 Creating New SCquenicess at ss ek rere io EER eos EE EREE R ER R EE ERRER Creating a New Sequence from Part of an Existing Sequence Creating New Sequences by Linking Noncontinuous Ranges of an Existing Sequence eee 47 Duplicating the Sequences Entirely ccc ee cess eseeeeseeseeeseeecseeseecseeesesseeaeaees 47 Reading New Sequences from a File 47 Renaming Sequences ieee 48 Restrictions for Naming Sequences 48 Hiding Sequences eee 48 Deleting Sequences 48 Changing the Order of Sequence Display 48 About the Target 0 cc eeeceseeseeseeneeee 49 Selecting Sequences as the Target of Editing 49 Selecting Sequences as the Target of Analysis i e a EE E E RI EA 49 Analyzing Multiple Sequences at Once sessssesessseseseeesesesesesesrertrssssesesesesesesesesesterersrsrersrererersrsrererorerereree 49 2 10 Searching for Sequence StringS ssesssesssesssesssesrreunrnernnernnurnnurnnnennnennnennneenneennnennnennnennnenn 50 Searching for Sequence Stein OS eran a E EE a E AEREE E E EAE E E RE 50 Jumping tothe Next Matehaere E S R R NE 50 Selecting All Matches at ONCEren deei aieia i A AAE EEE AEE A AE i 50 Selecting Sequences asthe Target of Searohiisss
63. Annotation Kind 4 Enter the Orient value 5 Click the OK button Assigning Annotation Entries to Multiple Ranges of Selection at Once 1 In the Sequence View select several ranges of a sequence 2 Click the go button on the toolbar Each annotation entry is named Unknown Editing Annotation Entries 1 In the Sequence View select an annotation entry you want to edit 2 Double click the annotation entry Alternatively you can right click the annotation entry and select the Edit Annotation menu item The Annotation dialog box appears as shown in the figure The Annotation Setting dialog appears Annotation Name 507 Annotation Kind GDS Link URL fittp muncbinlmnih gov entrez viewer foei val P54231 Annotation Range 262 1224 nput annotation range 1 3054 Orient _ _ _ _ __ Ga c none Part Range 4 Start End Add 262 1224 Delete Edit Comment i Key Value I Add codon_start 1 db_xret SWISS PROT P54231 pee db_xref PIDg1261961 e db xref PlD2234046 gene SOX 2 Edit product SOX 2 protein c translation MYNMMETELKPPGPOQTSGGGGGGGGNSTAAAA Line Width Z Part Width Color NNT Color Setting ok Cancel 3 To add a part click Add under Part Range to display the Add Annotation Part Dialog Specify the range for the part then click OK to return to the Annotation Setting dialog Add Annotation Part Dialog Input New Annotation Part Range 1
64. Click the Sequence tab SS xj Fon Sequence Foking Aue Display Mode DNA r ANA I Show oigna sequence I Show complementary sequenc Multiple Sequence Color Backgound Foregound FF Perfect match FE F Michmas 5 D F Mschiessihsn o fi ie F Coise Sequere Backgound Foreground Irhakze Use at Detours wh ol 3 The number in the Multiple Sequence Color indicates the matching rate To its right the display color is shown Additionally in order to enable this setting the next time the program starts up Click Use Default Also click Initialize to restore the factory setting Analyzing a Selected Range In the alignment display mode you cannot perform other types of analysis unless you cancel this 1 Select a region you want to analyze as shown in the figure Sequence TLYFIFGIWS GLLG TSLSL MIRTELGOPG SLLNDDOLYN VIYT AHAFY MIFFLS Sequence TLFFIFGIWS GLLG TSSSL MIRTELGOQPG SLLNDDOLYN VI T AHE He AAHE Y MIFFL Y MIFFLY Y MIFFLY F F Sequence LFFIFGIWS GLLG TSSSL MIRTELGQPG SLLNDDALYN IVT AHAF Sequence AFFIFFIWS GLLGTTSSSL MIRTELGQPG SLLNDDDLYN VIYT F 70 80 90 100 110 Sequence IGGFG NWLI PLMLGAPDMA FPRMNNHSF CLPPSETLEE TSMBYESEYE TEWTY Sequence IGGFG NWLI PLMLGAPDMA FPRMNNWSF CLPPSLTLEL TSWAYESGYG TOWTY Sequence IGGFG NWLT PLMLGAPDMA FPRMNNHSE CLPPSLTLLE TSAS YESGYG TAWTY Sequence ANWLIPNWLT PLMLGAPDMA FPRMNNHSE LLPPSLILLE TSAS ESGYG TOWTY 130 140 150 160 1
65. EEN EE 277 Add Spirals Adjust a Figure Chan Bea BiG ures ecco cues A AA A A A AEA E E EAA ER E EE 6 6 Printing Figures 6 7 Working with Templates 2 00 cccteccecceed cevestecceveenes cevestes cevested cevesnedceeeened ceresnes Cevestedeeeesteeeneeeter 281 Export a Template 281 Timp ort a Template crossan seven cuss ex ceca EE EE AE AEE voce teevelen avs E AEE 281 6 8 Exit Plasmid Map Drawing ccccesseseceseeeeeeeseeeeeeeeeeeseeeseeseseseeeseeeseaeseeeseaeeeseseanseseseaneeeeeees 282 Chapter 7 TUL OMA creena eE Ea a eGo 7 1 Before Starting the Tutorial sssssssseununnnnnnnnnnnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nna 284 7 AL About Installation eae EESE AAN E N EARN 284 Fel 2 Data Used athe Tutorials 45 3505 a Sa E A E E 284 Pele SAMI AL SOU Y e EE e EA doles scour vi ssuetboes coset eu cos A E boas sone EE E slates ameeees 284 1 2 ORF Seathan ohi anea arada sue dod shbuuedd su unduveba aaan eaaa iaiu 286 17 21 Starting DNASIS MAX oen aee aE EE EEE ESEE E EAE EEA ES EEE EEES EE E E eaae 286 72 2 Using the Editorto Open Sequence FleSirmeonvieiiii i ea a EAEE OEE A A KAVE 286 MPAA RUNMING ADI tA Saa e EEA AEE E E A 286 7 2 4 Running Translation 00 288 7 2 5 Displaying Only the Longest ORF 7 2 6 Entering the Amino Acid Sequence for Selected ORFs into the Editor 290 72 7 Running Amino Acid Mott See e dates sauiceyosacesacenscscess
66. File Read and register data from a GenBank FASTA file Blank Creates an empty database In the combo box select either DNA or amino acid sequence database Filtering Optional Set a filter used to add entries to the database Filter works only on GenBank format You can select one of the following four conditions Division Filter by Division field Definition Filter by term in Definition field Keyword Filter by term in Keyword field Organism Filter by Organism field Chapter 5 Databases 229 Comment Enter a comment You can leave this field blank In house Creates a database to store in house data such as experimental sequence data available in house Selecting the In house tab in the New Database dialog box displays the following dialog box x Pitie Intone w MES Date Sar Bist Nuiessde C Bit pro Aod C hanta te Mercier F f f J Item Description Name Enter the name of the database Data Source Set a DNA sequence or amino acid sequence and initial data Blank Nucleotide Create an empty DNA sequence database Blank Amino Acid Create an empty amino acid sequence database FASTA file Nucleotides Read DNA sequence data in the FASTA format FASTA file Amino Acid Read amino acid sequence data in the FASTA format Comment Enter a comment You can leave this field blank 230 Databases 5 3 Registering an In House Database Register a DNA or amino acid sequence on the sequence editor
67. Find Range field 5 Click the Find button Ifa match occurs the window automatically scrolls to the range of the match To jump to the next match select Sequence and then Find Again or press the F3 key The next match actually refers to the sequence reached in the process of searching the list of sequences currently displayed on the window in the following order from left to right and from top to bottom It is also possible to search for at once all matches from all the sequences that are currently displayed 52 DNASIS Basics 2 11 Annotations About the Annotation You can add information to a specified range of a sequence For example the GenBank format has the FEATURES table which contains pieces of information about a sequence such as the CDS region and promoter region DNASIS MAX is designed to extract information from tables and display it graphically A description or other information to be associated with a sequence or a region of a sequence is called an annotation The individual pieces of information added to describe the annotations in detail are called annotation entries 10 20 30 40 50 fe a aiaa adaa Sequence tgctggtggg atcasagcgc agtetcctec ggcggggagc ttegaacest acggueagt Annotation Annotation_ amp Annotation_B Annotation S3 Annotation entries Creating New Annotations Annotation Annotations 1 Select a sequence for which you want to create a new annotation 2
68. Hide E Sequence View Show Hide fp Data List Window View F Analysis Result List button Icon DNA View Mode button Function Shows DNA in sequence view or in alignment view Amino Acid View Mode button Shows amino acids in sequence view or in alignment view Sequence View Mode button Shows sequence in sequence view pane If you click this button while in trace view or alignment view the mode will switch to sequence view Trace Window View If this bu ton is on and a trace file available a chromatogram will be seen The DNA and amino acid toolbars will be hidden Alignment Window Show Hide If this bu ton is on the alignment window will be shown Analysis Button View Show Hide If this button is on the analysis button view will be shown Comment View Show Hide If this bu ton is on the comment view will be shown Map View Show Hide If this bu ton is on the map view will be shown Sequence View Show Hide If this button is on the sequence view will be shown Data List Window View Click this button to show the data list window Analysis Result List button Click this button to show the analysis result list Other Toolbars Toolbars provide icons for frequently used functions Standard Toolbar Icon Function i a CC Opens a new empty window S Opens a sequence file or project W Saves a project disk
69. Plasmid Mode creating and editing normal figures is not allowed When there is no plasmid circle in the editing area such as after deleting one click kad to open a dialog to create a new plasmid circle The operation is as follows 1 Click when there is no plasmid circle in the editing area The Plasmid Component dialog will appear x Plasmid tne Piscmad name Placmad bese length fon Format Stat pant Degee Item Description Initial setting Plasmid Name Specifies the plasmid name using up to 50 single byte characters to show in the center of the circle Plasmid base length Specifies the plasmid base number 4000 Minimum value 100 Maximum value 99999 Format Selects the displaying format of plasmid base number base Start point Specifies the start position of the base sequence from 0 to 359 0 When tabs other than the Plasmid Tab are selected it is possible to set the line type or thickness 2 Input necessary information and click OK A plasmid circle will appear However when unknown is specified in Format the base sequence number will not display Add Restriction Enzyme 1 Click Eze on the Toolbar and click a point on the plasmid circle circumference The Restriction enzyme Component dialog will appear Chapter 6 Lerstration enzyme Component Create Plasmid Maps 271 bx Rennien eame ure hatar amare nyre hanar eee peon
70. Result list into DNASIS Close button Click the button to close the dialog For details refer to 3 43 NCBI Entrez Search Chapter 2 DNASIS Basics 21 2 2 Entering Sequences Creating DNA Sequences 1 Select File gt New Menu and a dialog box entitled Welcome to DNASIS MAX will appear For Type select DNA and for Content select A new sequence then click the OK button 2 Anew untitled Main Window opens with a flashing cursor at position lin the Sequence view Pane a ald the p Somers p toe DFU ee an 7107 gt i e386 t gt BSS D sOw as gt Lf J marts rem Loti areren t agar H Bits jo DMA Sesh a Dra Corpse s OPA huig Segue im Anowterd Bare Arowhad Sood 5 rer Urost Avectend Whee Stoer L Dw atene d Orre a taet Target Untied Poster 1 be mare 3 Any character entered from the keyboard is inserted at the Insertion Pointer which is a vertical bar flashing at the 1bp point in the Sequence View You can also paste a sequence from the Clipboard Characters You Can Use for DNA Sequences The following is a list of characters you can enter in DNA sequences The input process is case sensitive uppercase and lowercase characters are distinguished However the analysis process is not case sensitive users are allowed to assign their own meanings to uppercase and lowercase characters R Complex code re
71. Selects the direction of the annotation Clockwise forward Counterclockwise backward Non direction When tabs other than the Annotation Tab are clicked it is possible to change the arrow line type and color 2 Input necessary information and click OK The annotation will be changed When non direction is specified or the length is shorter than the arrowhead the arrowhead does not appear When the same value is designated for the Annotation start position and the Annotation end position the annotation is represented as a line Delete Objects It is possible to delete selected objects plasmids restriction enzymes DNA and annotations When a plasmid is deleted the relevant restriction enzymes DNA and annotations are all deleted When a DNA is deleted the base number of the DNA will be subtracted from the total base number of the plasmid and the object position after the delete position To delete an object select it and click X on the Toolbar Additionally deleting only the text area of an object is not allowed Import a File You can import external files in the dmp format by selecting Export in the File menu of the main window 1 Click on the Toolbar The dialog below appears 276 Create Plasmid Maps booker SMe ix amore E ao m 2 Select a file and click Open If there is a plasmid map being created the following message saying that the plasmid map being created will be destroyed will appe
72. Sequence0011 0 00646 0 031 Sequencel007 0 016 Sequence0017 ia 1 001 quence 024 a Added sequence 130 Details of Analysis 3 27 Sequence Assembly After importing sequences to be assembled or clustered into the project launch DNASIS Assemble from Analysis tools menu under DNA Multiple Sequence Explanation of the Result Window CL aiai n D p m o 4258 44 Jagna Map View Sequence View Map View Display the contig and fragments graphically Sequence View Display the contig and fragments Setting Parameters 1 Click the Sequence Assemble icon from analysis button view An Analysis dialog box will appear then click the Parameter button and the Sequence Assemble Parameterset Editor will appear Porometerset editor Parameterset Nene RS Parsneterset Type REKONAS Acsenble SOS S S Parameters Hin Overlap loreth fC MinMatch Rate FO ooo Homokey Compare Na EJ MaxMatch Compare NA 0 M Ck ow 2 Set each parameter 3 Click the OK button Chapter 3 Details of Analysis 131 3 28 Clustering This function sorts all the sequences displayed in the window into some clusters according to the similarity of sequences From the list you can identify the cluster to which each sequence belongs The tool is launched from the Analysis tools menu under DNA Compare Explanation of the Result Window From left to right each cell shows the following the input se
73. The analysis name for the resulting annotation is called Annotation 1 4 Using its analysis name select an annotation and click p on the toolbar so that an annotation entry is added to the specified annotation Chapter 2 DNASIS Basics 55 2 12 Printing Printing the Map View After clicking in any blank part in the Map View select File and then Print or click the Z button on the toolbar Printing the Sequence View After clicking any blank part in the Map View select File and then Print or click the amp button on the toolbar Printing Only the Current Range of Display 1 Determine any part you want to print by using the layout view 2 Select File and then Print Page 56 DNASIS Basics 2 13 Projects About the Project The term project refers to a collection of the sequences that have been opened in a single editor along with their analysis results DNASIS lets you store sequences on a project basis Such a project is given a dnasis extension Saving Projects 1 Select File and then Save Project or click the button on the toolbar The Save As dialog box then appears 2 Specify the storage location and file name before clicking the Save button Opening Projects 1 Select File and then Open or click the button on the toolbar The Open files dialog box then appears 2 Specify the location for a project you want to open and the file name before clicking the Open button
74. Together with the sequence this view displays the proteolytic enzyme name and the proteolytic site Clicking the mouse on a proteolytic enzyme turns it to the selection color Selecting Proteolytic Enzymes to Be Searched for Proteolytic enzyme is registered with the Proteolytic enzyme database Only the enzymes selected from the database are searched for The more enzymes to be searched for the longer it takes to perform the search and display its result It is recommended that you only select Proteolytic enzymes you want to search for before starting actual search Select the Proteolytic enzymes according to the procedure 1 Click the Proteolytic Recognition Site Search icon and an Analysis dialog box will appear Click the Parameter button and a Proteolytic Site Parameter Editor will appear KRIX Acrosin RIX CathepsinB1 CathepsinG LYFIX CathepsinG Chymosin FIM Chymosin WChymotrypsind FYWIX ChymotrypsinA chy motrypsinc FYL X ChymotrypsinC WClostripain RIX Clostripain Show Checked Cocoonase KRIX Cocoonase Z CyanogenBromide MX CyanogenBromide Show Unchecked M Elastase AX Elastase Enteropeptidase DDDDK I Enteropeptidase RIX a a ma Proteolytic Enzyme Database Manager 2 Proteolytic Site Parameter Editor displays the proteolytic enzymes registered A restriction enzyme is selected when the preceding check box is marked with a checkmark Place a checkmark on the check box for the restriction enzyme you want t
75. Tree icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a Multiple Alignment Parameter Editor will appear Multiple AlignmentPaeameterEdtor _ x GereralSettines PaimiseAbennent NultiokeAlernent ProteinGep Tros C Phykoreii tres Enummi Hurter of bootstrap miake 1 10000 fio Seed no 11 700 All I Eechxhe pozitia with gapa I Corect for multiple nisttutiong 2 Click the Tree tab 3 Select the Bootstrap tree Number of bootstrap trials The number of random trials Seed No This is the random number seed for the random number generator 124 Details of Analysis Set these parameters 4 Click the OK button 5 Click the Phylogenic Tree button to start analysis Chapter 3 Details of Analysis 125 3 24 Create a Phylogenic Tree for Manually Edited Alignments After editing the contents in Alignment View a new phylogenic tree is created from the results Procedure 1 Click Multiple Alignment amp Phylogenic Tree in the Analysis Button View 2 The Phylogenic Tree appears Result Window Description 0 Multiple AlignmentTre iew Help Eile Edit View He t pf eseraanN eH ee 009 0 020 029 Sequence0000 0 059 0 128 0 020 0 195 l 0 308 Sequencel0 11 Sequencel005 Sequencel006 0 171 Sequencel001 0 166 0 137 Sequencel003 Sequence 028 r 0 049 Sequence 010 0 064 Sequencel 012 0 170 Sequen
76. Using the mouse Press the mouse s left button at the starting point and move the mouse to the ending point and release the button You also can select more than one line at a time Automatic scrolling starts if you move the mouse cursor outside the Sequence View Using the keyboard Move the Insertion Pointer to the starting point and while holding down the Shift key press the cursor move key Selecting a specified range Select Edit and then Select Range and then enter a bp measured value to specify the range you want to select Expanding a selected range While holding down the Shift key click the mouse s left button or press the cursor move key In contrast however it is impossible to reduce the selected range In that case first cancel the selected range and then redo it Selecting an entire sequence Select Edit and then Select All Canceling the Selection Click somewhere on a sequence or press the cursor move key Deleting the Selected Range To delete a selected range press the Del key or the Back Space key For more than one sequence be sure that the sequence is handled as the target that is its sequence name and analysis name are underlined Replacing the Selected Range To replace a selected range enter data from the keyboard or paste it from the Clipboard onto the selected range For more than one sequence be sure that the sequence is handled as the target that is it sequence nam
77. a List item then click to display the Select Enzyme dialog 3 If you want to register an existing restriction enzyme select Import to select a file you want to register Name Recognition Sequence New Aarl CACCTGC GCAGGTG 7 not identified Aatl AGGICOT 6 blunt cut Dalsi Aatll GaceTic 6 3 extended Aaul TIGTACA 6 5 extended ieee Accl131 AGTAOT 6 blunt cut a Accl61 TGCIGCA 6 blunt cut Inport Acc36l ACOTGONNNNINNNN NNNNNNNNGCA 14 5 extended Acc6Sl QGTACC 6 5 extended Eoo AccBII GQGYRCO 6 5 extended AccB7I OCANNNNINTGG 11 3 extended AccBSI OOGIOTO GAGICGG 6 blunt cut Accl GTMKAC 6 5 extended Accll caica 4 blunt cut a O Pa tev When you want to create a new restriction enzyme select New The New Enzyme window appears as shown in the figure Enter the required items and click the OK button 96 Details of Analysis Enzyme Name p oa Restriction Site Normal Saas Complementary yaaa The number of bases J Kind of Cut Notidentified OK Cancel Selecting a Restriction Enzyme to Display 1 For the enzyme restriction result in sequence view select the sequence name and analysis name then click the Result List Dialog button Eile Edit View Help Ee ajola Pattern Bases Kind of Cut __ ofCuts __Positions_ BamHI eleatec 5 extended Bell algatct 5 extended Hind I alagctt 5 extended Hpal ttlaac KpnI eetacle Mul alcecet Neol cleate
78. a come Moditication Date Item name Parameter name URL of NCBI Entrez Description Set the URL of the NCBI site Maximum Entries Sets the number of entries actually obtained from hits not affecting the number of hits displayed Modification Date Sets the dates of entries actually obtained from hits not affecting the number of hits displayed Explanation of the Result Window GenBank report button Item name Parameter name Result list Search expression Column Rheum x cultorum NADH dehydrogenase subunit F ndhF gone partial ode chloro header Pisum sativum NADH debydrogenese subunit F adh gene partial ods chloroples AF238055 Hydraste canadensis NADH dehydrogenase subunit F ndhF gene partial cds chic AF286310 Homo sapiens eppr 3 EPPING mRNA complete cds Result list AF173830 AF257497 AF202305 AF292394 NM 021053 AY005335 aAyousaa 2 AY005333 AY005331 j SEG_AY0053305 6 AF0740 7 AF233403 AF283407 9 AF252955 AF231910 Methanosarcina ther mophde acetyl CoA decarbonylas Homo sapiens chromosome 8 map 8q24 3 clone CTC synthase beta subuni F14 complete sequer Stromayloceritrotus purpuratus KRP170 mRNA complete cds Strongyboentrotus purpuratus KRP110 mRNA complete cds Mus musculus thymic stromal cotransporter Tecot mRNA f ORFG and ORFOB genes eene complete cds 60 and ORF61 genes complete ods JRF 4S gene complete cde Human herpesv
79. a format error and continues importing subsequent restriction enzyme data Skip All button Continues importing restriction enzyme data skipping all subsequent restriction enzymes which contain a format error Cancel button Cancels the importing of restriction enzyme data Clicking this button preserves the original restriction Chapter 5 Databases 247 enzyme data without importing any data Name Collision dialog box If the database already contains a restriction enzyme having the same name as that of the restriction enzyme being imported the Name Collision dialog box appears as shown below This enzyme is already registered Please select skip or overwrite Skip All Overwrite Overwrite All Cancel Button description Button Description Skip button Skips the restriction enzyme having a duplicate name and continues importing subsequent restriction enzyme data Skip All button Continues importing restriction enzyme data skipping all subsequent restriction enzymes having a duplicate name Overwrite button Overwrites the existing restriction enzyme with the imported one and continues importing subsequent restriction enzyme data Overwrite All button Continues importing restriction enzyme data overwriting all existing restriction enzymes with the imported ones Cancel button Cancels the importing of restriction enzyme data Clicking this button preserves the original restriction
80. annotations If sequences are separated by a line in a file all of those sequences are read into and displayed in one project Reading Files in the Old Version DNASIS Format This format is used for former versions of DNASIS DNASIS for Windows V2 1 or earlier The part ranging from a DNASIS line to the point immediately before a SEQ line is read as a comment while the part ranging from the SEQ line to is read as a sequence The file name without its extension is used as a sequence name Any sequence including a character that is not found in DNA sequences is regarded as an amino acid sequence otherwise the sequence is regarded as a DNA sequence Reading Files in Text Format Used for text files this format is different from any of the FASTA GenBank Flat EMBL PIR and former DNASIS formats Excluding the numeric data symbols and other characters not found in DNA or amino acid the entire file is read and displayed as sequence If even a single character typically representing an amino acid is present then the sequence is regarded as an amino acid sequence otherwise the sequence is regarded as a DNA sequence The file name without its extension is used as a sequence name The comment is empty Reading Trace Data Files in the ABI SCF and ALF Formats This deals with trace data files also referred to as waveforms chromatograms in the ABI SCF and ALF formats These files typically have the extension abi
81. as color can be changed The operation is described below 1 Select a spiral and click on the Toolbar The Plasmid Component dialog will appear Click the Spiral Tab Chapter 6 Gema ca ST Posin ant See x twaany nez we ta eo Spent a Spe dact _ Cote Anite cd mej Mate wed D ert lee baa Cob Spadive Coke SMD Seve es D Create Plasmid Maps 279 Item Description Spiral front Color Selects the surface color of the spiral Spiral back Color Selects the backside color of the spiral Another Spiral front Color Selects the surface color of the other spiral Another Spiral back Color Selects the backside color of the other spiral Spiral line Color Selects the line color of the spiral Another Spiral line Color Selects the line color of the spiral Frequency Displays the frequency value of the spiral Height Displays the frequency height of the spiral Width Displays the band width of the spiral When tabs other than the Spiral Tab are clicked it is possible to change the other properties 2 Input the necessary information and click OK The spiral will be changed 280 Create Plasmid Maps 6 6 Printing Figures Plasmid maps can be printed 1 Select Command gt Print in the menu 2 The plasmid map will be printed Chapter 6 Create Plasmid Maps 281 6 7 Working with Templates Data in the process of creation can be exported to templates or st
82. column header to sort the databases by date Comment Displays comments for the amino acid motif database if any You can click the column header to sort the databases by comments New button Creates a new database Clicking this button causes a new empty database to be created and added to the list Delete button Deletes the selected motif database This button is disabled if no database is selected You cannot delete a locked database Property button Displays the properties of the selected motif database This button is disabled if no database is selected or if more than one database is selected The Amino Acid Motif Database Property dialog box appears View button Displays motif data from the selected motif database This button is disabled if no database is selected or if more than one database is selected The Amino Acid Motif Database dialog box appears Import button Imports a motif database from an external file Clicking this button opens a file dialog box that lets you select the motif database to import DNASIS does not import a motif database if it already contains a database having the same name Export button Exports the selected motif database This button is disabled if no database is selected or if more than one database is selected Clicking this button opens a file dialog box that lets you specify where you want to export the motif database to DB Path button Allows you to specify
83. displays the amino acid sequence for the selected portion in the Sequence View as shown in the figure Untitledoor Sequence E 10 20 30 40 50 Untitled001 Sequence TSWATRSTRA STRTAPLRCS PCTAT ceeeeeeeee seneeeeees Chapter 3 Details of Analysis 75 3 6 Base Content This function analyzes and displays the ratio of bases that comprise DNA sequences The result of analysis is displayed in another window Explanation of the Result Window Base Usage Analysis mode Mode Normal Total Base 3054 Code 4 H G TCU R A G C TCU WOAFTCU S G C K G TCU WCAC B C G T U D A G T U HCAZC T U CA C G NCA C G T U Total 3054 File menu Description Export Exports the data in the window into a text file Print Prints the window Print Preview Displays a printing image Print Setup Provides various print settings Exit Closes the result window Edit menu Description Copy Copies the data in the window as a tabbed character string into the Clipboard View menu Description Toolbar Toggles the toolbar to display hide it Status bar Toggles the status bar to display hide it Help menu Description About DNABasicAnalysisViewer Displays the version information of this analysis function in a dialog Contents Displays online help Button Description H Export button Provides the same function as the Export menu Prin
84. existing cluster DB Beah t lt Cst Clustering Conditicess Score is more then 200 and Overlapping length for query length is more than fa x Help Item Description Sequence Type Specifies the type of the input sequence Nucleotides or Amino Acid Mode Selects the type of clustering The following two modes are available Clustering only input sequences each other Performs clustering between sequences in the Sequence Editor An existing cluster representing sequence database is not used Clustering with existing cluster DB Performs clustering between a sequence in the Sequence Editor and an existing cluster representing sequence database The cluster representing sequence database will be updated as a result of clustering If this mode is selected the Browse button is enabled Clicking the Browse button displays the database selection dialog box in which you can select a cluster representing sequence database Score is more than Specifies a BLAST search score used as a basis for clustering Overlapping length for query length is more than Specifies the ratio of the length of the matched sequence in BLAST search according to the entire query length of the sequence This value is also used as a basis for clustering 216 Details of Parameters 4 27 BLAST Search and Extraction Item Description BLAST Search Displays a dialog box used to set parameters for BLAST search Mak
85. functions available to you in DNASIS MAX Each analysis category is indicated by a tab button and clicking the analysis category name displays the sub menu of functions in that category Analysis button L Scroll button PA Set Pa beeper ee oum ein Pent Pat enre fot wares rga anman natok Sea ewes Perese Oter Analysis Category Right clicking the icon displays a menu as shown below DNA Basic Menu name Function Small Icon Displays a shrunken icon in the leftmost corner of the view Large Icon Displays an enlarged icon in the middle of the view k Delete Deletes the analysis icon p Large Icon Hipias edeni Delete Duplicate Copies the analysis menu DNA Compare DNA Multiple Ser Duplicate Rename Changes the analysis name Eee aes ee Rename Kamnoner Bae Parameter Displays the Parameterset Editor for changing the setting AminoAcid Searc A Parameter AminoAcid Comp Analysis Dialog Analysis Dialog Starts an Analysis dialog aL Seen Chapter 1 1 3 Toolbars Switch Pane Toolbar Window Descriptions 5 The Switch Pane Toolbar is for controlling and switching between the different views in the Main Window DNAView Mode button Amino Acid View Mode button Sequence View button Trace Window View Ba Alignment Window Show Hide fait Analysis Button Views Show Hide Comment View Show Hide E Map View Show
86. gap information are also duplicated although the trace data or annotation is not duplicated Reading New Sequences from a File There are two ways of reading sequences from a file and adding them to a window 1 Select File and then Open or File and then Import Sequence before selecting files you want to read from a list of files In this case you can also select several files at the same time 2 Using Windows Explorer select a file you want to read and drag and drop it to the DNASIS window It is also possible to drop in several files at the same time 48 DNASIS Basics Refer to 1 7 Data List Window Renaming Sequences You can change the name of any sequence For details refer to Renaming Sequences in 2 4 Editing Sequences basic Restrictions for Naming Sequences Sequence names have restrictions concerning their length and font type Hiding Sequences You can temporarily hide any sequence and the analysis result for the sequence 1 Right click the name of a sequence you want to hide 2 From the pop up menu select Hide as shown in the figure AF165047 Sequence 4F165048 Sequence 4F165049 Sequence AF165050 o gt ence Aric A nce Move Down E AF165047 Sequence AF165048 Sequence AF165049 Sequence AF165050 Sequence 1 AF 165051 Sequence 3 This action hides sequence and its analysis result To redisplay the hidden sequence and its analysis resul
87. gtctataaga gaattatata tttctaacta tataacccta ggaatttag Importing a Vector You can add a vector by importing a vector information file exported from DNASIS MAX on another PC In the Vector Database Manager click the Import button and specify a file Exporting a Vector You can output vector information into a file so that you can import a created vector into DNASIS MAX on another PC In the Vector Database Manager click the Export button and save vector information to a file Chapter 5 Databases 239 5 5 Amino Acid Motif Database The Amino Acid Motif Database Manager lets you browse and manipulate a motif database for amino acid sequences as well as browse and manipulate motif data You can create edit delete import and export a motif database Window Description Areno Acad Motit Database Manager User User2 DE Path fa PROGITE Release 13 Item Description Motif Database Displays a list of amino acid motif databases Name Displays the name of the amino acid motif database Any locked database is shown with a padlock icon to the left of the name You can click the column header to sort the databases by name of Motifs Displays the number of motifs registered in the amino acid motif database You can click the column header to sort the databases by number of motifs Modified Displays the date on which the amino acid motif database was modified last You can click the
88. in importing the sequence into the Project Since this function directly connects to the NCBI s Web site you need to set the Internet configuration parameters When using a proxy server you also need to set HTTP Proxy in the Internet Options Explanation of the Search Window Joining condition value input field Database nuc kote z Keywords AR Field word Operator _ Ewn Search target field Search Cos E Hob f Item name Description Parameter name Database Selects the type of the database as the target of search Nucleotides Proteins Operator Chooses from OR AND and Delete this deleting one line Search target field Sets the field as the target of search Joining condition Chooses from the following is is not begin w and does not begin w Value input field Enters a search word date number and other data New Keyword button Adds one line to the keyword You can set up to 20 lines Clear All button Deletes all keywords that have been set Search button Starts search under the preset search condition Options button Opens the dialog box that enables option settings Close button Closes the dialog box without performing search What has been entered is saved Cancel button Closes the dialog box without performing search What has been entered is not saved Help button Displays online help Operators Search by specifying multiple
89. in the Amino Acid Symbols field in the Translate View Property window as shown in the figure Translate View Property Show Frame F Amino Acid Symbols C One Letter A E T MV Frame F Frame 3 Three Letter Ala Glu Thr Amino Acid Colors IV Colorize map view 3 Click the OK button Changing Codon Table You can select a codon table for translation from the registered codon tables 1 Click the Translation icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear 2 Select a codon table for translation in the Codon Table in the Translate window as shown in the figure Codon Table J omei 3 Click the OK button Changing the Display Color of Amino Acids You can change the display colors of amino acid sequences in the result of translation The initial setting provides four different colors 1 Selects View and then Preference Alternatively you can click the g button on the toolbar 2 Select the Sequence tab in the Preferences window 3 Select the Colorize Sequence check box then select Amino Acid 4 Select amino acid in the combo box for selecting amino acid 74 Details of Analysis Font Sequence Folding Puller I Show original sequence I Show complementary sequence r Multiple Sequence Color I Pertect match F Makh sre than 51 8 y Ma
90. known for a long tine 1 that potential N zlycosylation sites are specif ic to the consensus sequence Asn Xaa Ser Thr It must be noted that the presence of the consensus tripeptide is not sufficient to conclude that an asparagine residue is glycosylated due to the fact that the folding of the protein plays an important role in the regulation of N slycosylation 2 It F Displaying a List of Search Results For the motif result in sequence view select the sequence name and analysis name then click the Result List Dialog button This displays a list of motifs retrieved File Edit Help ASN_GLYCOSYLATION NE PIISTIT P CK2_PHOSPHO_SITE ST 2 DET EF_HAND iD ONS ILVFYWT DENSTG DNOGHRK GP LIVMC DE posTAGC 2 DE LIVMF YY MYRISTYL Gpp 27 TSTAGCN PKC_PHOSPHO_SITE ST RK Chapter 3 Details of Analysis 147 3 34 Common Motif Search Analyzes motifs common to multiple sequences Searches can be done using the database or by specified patterns Common motifs to either DNA sequences or amino acid sequences can also be searched Result Window Description ails w Je ye CER LESA EET TEELT Jop ES SeGn at ONA Bae OMA Sowth w w tey he tey sep De ba goco Sobe Morsa f OCF cs gone gorgot piy c coig tem Sabet Morsa SL emetos Sieti asitie Map View Displays the common motifs of the pin search
91. motif You cannot edit this item if the database is locked Pattern Assistant Beginning of the sequence Any character End of sequence Or Grouping Character Class Character not in the list Match 0 or more times Match 1 or more times Match 0 or 1 times Match exactly n times Match at least n times A drop down list which helps you specify a motif pattern You cannot use this list if the database is locked The available items include Enters a caret character at the beginning of a sequence Enters a period which matches any character Enters a dollar sign at the end of a sequence Enters a vertical bar which means or Enters parentheses for grouping Enters brackets which means a range of characters Enters a caret and a space within brackets which means characters other than those in the specified range Enters an asterisk which indicates zero or more repetitions Enters a plus sign which indicates one or more repetitions Enters a question mark which indicates zero or one repetition Enters braces which means n repetitions Enters a comma which means n or more repetitions Motif Pattern Test Sequence Enters a sequence used to test the pattern Clicking the Test button causes any section that matches the pattern to be highlighted Test button This button is used with the Motif Pattern and Motif Pattern Test Sequence fields to test the
92. not performed although it is specified Output Options Not used in DNASIS MAX Do not select the Output to Others folder check box Selecting this check box will result in malfunction Default button Returns parameters to default values Chapter 4 Details of Parameters 183 4 9 ORF Open Reading Frame Codon Table hhitial Codons Standard z Ei oeei Item Description Codon Table Selects a codon table To check the contents of a Codon Table press at the right edge of the Codon Table box The Codon Table Editor will appear Initial Codons Shows the initial codon name The contents of the selected initial codon will be displayed To check and edit the contents click The Initial Codon dialog will appear The one with a check in the check box is the specified initial codon Open Reading Frame Search Result List File Edit View Help aS amp 2 v Te slel cho 34479 26 ATGTACAACATGATGGA 3407080 ATGATGGAGACGGAGC 33939 61 ATGGAGACGGAGCTGA 29837 39 ATGAACGCCTTCATGGT 29373 86 ATGGTGTGGTOCOGOGG 28088 38 ATGGCCCAAGAGAATC 2728950 ATGCACAACTCGGAGA 2301680 ATGAAGGAGCACCCGG 20667 15 ATGAAGAAGGATAAGT 18757 99 ATGGCGAGCGGGGTCG 17175 27 ATGGACAGCTACGCGE 1647055 ATGAACGGOTGGAGCA 1570053 ATGTGCAGCGCTCGCA 1538648 ATGATGCAGGACCAGO 15255 29 ATGOAGGACCAGCOTGG 14550 27 ATGAACGGCCGCTTCTC 13140 07 ATGCAGCOCATGCACO 12783 64 ATGCACCGCTACGACG 1121799 A
93. number Insert end position Specifies the end position of the insertion region Specified position Minimum value 1 Maximum value Plasmid base length number DNA base length Specifies the number of bases to inserting DNA This item is required 1 Direction Selects the insertion direction Clockwise forward Clockwise forward Counterclockwise backward Non direction 272 Create Plasmid Maps When tabs other than the DNA Tab are selected it is possible to change the line type and arrow thickness 2 Input necessary information and click OK The DNA will be added and the DNA name will appear outside of the circle The specified restriction enzymes and the restriction enzymes in the specified area will be deleted Also the difference between the number of DNA bases to insert and the number of bases of restriction enzymes in the specified region will be added to the total number of plasmid base number and the position of objects after the insertion point When non direction is specified or the length is shorter than the arrowhead the arrowhead does not appear Adding an Annotation 1 Click E on the Toolbar and drag clockwise on the plasmid circumference from the start to the end position The Annotation Component dialog will appear Item Description Initial setting Annotation Specifies an annotation of up to 50 single byte characters Insert start position Specifies the start
94. of a query sequence Query Identifier Shows the identifier of a query sequence Specifying a Database to Be Searched Select a database as the target of homology search You can select more than one database at one time 1 Click the BLAST Search amp Report button under DNA Compare in Analysis Tools menu An Analysis dialog box will appear Click the Parameter button and Analysis Parameters will appear 2 Select BLAST Search and click Set to display BLAST Parameters 136 Details of Analysis est Parameters Program name bissin Detail Expectation vaka T0 Oaa I Fie query sequence Descaptions 50 I Inchade pap n abgrmert Aigmerts 50 Nucleonde Database BCT InHouse NA v MiM UniGere_He_Unig Select Al Deselect All 3 In the Nucleotide Database field place a checkmark in the check box for the target database 4 Click the OK button to complete the setting Setting Extract Conditions 1 Click the BLAST Search amp Report button and an Analysis dialog box will appear and Analysis Parameter will appear Click the Parameter button 2 Select Make Report and click Set The Collect Homology Results Parameter Editor window appears Collect Homo lesults Parameter Editor Refer to Collect ae e Baal ier Homology Results Primary Keyword MatchinePercentaee gt Parameter Editor Secondary Keyword Oversppre z in 4 27 Blast F Pick up all items wit
95. on from the next time on when the analysis button is clicked analysis will be performed without showing this dialog Parameter button Starts a parameter dialog Execute button Performs analysis After analysis the dialog closes Help button Opens the online help Close button Click the button to close the dialog Settings made in the Analysis dialog are saved Chapter 2 DNASIS Basics 17 Chapter 2 DNASIS Basics 18 DNASIS Basics 2 1 Starting DNASIS From the Start menu select the following items Program DNASIS MAX and then DNASIS MAX The main window will open but behind a dialog box entitled Welcome to DNASIS MAX Welcome to DNASIS MAX Oe DNA F Other Project Type Content oe Anew sequen NHO Amino Acid 4c Sequences from files ice Retrieving sequences from database Gir Retrieving sequences from NCBI Entrez fc Open existing project 2 C HSK_DB TutorialD ata MuttipleAlignment dnasis 3 C HSK_DB TutorialD ata Calmodulin dnasis 3 E HSK_DB TutorialD ata Calmodulin dnasis a E HSK_DBST utorialD ata T yrosineKinasePhosphorylationSite dnasis 3 E SHSK_DB TutorialD ata MultipleAlignment dnasis 2 E HSK_DB TutorialD ataMl6 dnasis Item Create a new project button Description Creates a new project Type button Sets the sequence type An error will occur if you specify a different sequence from the type tha
96. scf or alf A sequence that has been base called in advance into the file is extracted as a DNA sequence The file name without its extension is used as a sequence name The comment is empty The trace or waveform data is also extracted and stored in the project and can be viewed along with the sequence in using the Trace Mode Reading Multiple Files You can enter multiple sequences into a single project With the DNASIS Main window open and DNA or Amino Acid mode selected select File from drop down menu of Main window and then Open and choose multiple files from the open files dialog box and click OK Alternatively select File from drop down menu of Main window and then Chapter 2 DNASIS Basics 27 Import Sequence You can also drag and drop a file with multiple sequence records from Windows Explorer These sequences are then added in the window oz Untitled DNASIS BEE Ele Edit Sequence View Help Die eee S S rao es eae os ESE aa wias JAFO11753 lt Trimming w 2 Sequence gcc gocece tg tgggggo t tecectgt Sequence tgecegeeec tgggge ti tecectgt Sequence gee gecece tg tggggge t tococtgt Sequence gee gecece tg tggggge t tecectgt Sequence gee gecece tg tggggge t tecoctgt Sequence boo geceee tgggggc t tecectgt a AB016785 Sequence totte cgc gogtct gcc t tag tgtegtgc AB031663 Sequence DEECEEIR gogtct t tag tgtegt c Sequence t
97. selected in the features list Creating a New Vector To add a new vector perform the following steps 1 In the Vector Database Manager click the New button Chapter 5 Refer to Importing a sequence from an External Definition File in 5 4 Vector Database 2 The New Vector dialog box appears Erter Nem Vector Mares Type of Vector Crosly z Lodo zj t Definition Ti Access ion Feomres Features Start Erd Add oveet_ You can also import a sequence from an external definition file 3 Specify the required items in the New Vector dialog box See Table 1 for the required items Table 1 Databases 233 Item Required Enter New Vector Name x Type of Vector x Sequence x Definition Accession Features Note A checkmark x indicates a required item 4 After specifying the required items click the OK button 5 The vector list in the Vector Database Manager will display the name of the added vector Vector sequence Table 2 lists the characters you can register as a vector sequence You can only register a character that is defined in Table 2 A a M M C c S S G g W W T t B B U u D D R r H H Y V V K N n Table 2 Modifying Vector Information To update information about a vector perform the following steps 1 Select the vector you want to update from the vector list in the Vector Database Manager 2 Modify information as requir
98. tatecagasg ccgaggccec gagctattcc agaagtagtg aggagecttt tttegagecc tagactttts ggcattcceg tactettget aaagccacca tegaagacec caaaaacata cgaceccatt ctatccactg gaagatggaa ccgctggaga gcaactgcat agagatacec cctggttcct ggaacaattg cttttacaga tacacatatc gaggtegaca tcacttacec tgagtacttc gaaatstccg ttcegttsgc agaagctats v Edit New Delete Import Export gctagcccgg gctcgagatc tacgatctgec atctcaatta Reference Help Button Description Edit Modifies the vector New Adds a new vector Delete Deletes the vector selected in the vector list Import Imports a vector from a specified file to the database Export Outputs the vector information selected in the vector list to a file so that DNASIS can import it into another PC Close Closes the Vector Database Manager Reference Displays reference information for the vector selected in the vector list Help Displays online help Cloning Site Specify cloning site settings for a vector Button Description Edit Displays the screen used to update the cloning site selected in the cloning site list Add Displays the screen used to add a new cloning site Delete Deletes the cloning site selected in the cloning site list Features Specify feature settings for a vector Button Description Edit Displays the screen used to update the features selected in the features list Add Displays the screen used to add a new feature Delete Deletes the feature
99. than one exclamation mark 7 The Complementary text area contains a recognition sequence having a length different from Chapter 5 Databases 245 Item parameter Description that of the sequence in the Normal text area When you click the OK button DNASIS checks for a duplicate enzyme name If the database already contains a restriction enzyme having the same name DNASIS shows a dialog box with a message stating that the restriction enzyme name is a duplicate and you cannot register the restriction enzyme Cancel button Cancels the creation of a new restriction enzyme and returns to the Restriction Enzyme Database Manager window Example of Registering a Restriction Enzyme For EcoR The recognition sequence has a palindrome structure Enter G AATTC in the Normal text area 5 GIA A TTC 3 3 S m m A A G Poe 5 For Mbo ll ee ae i 3 N 3 CTTCTINNNNNNN The recognition sequence does not have a palindrome structure Enter GAAGANNNNNNNWN in the Normal text area and N NNNNNNNTCTTC in the Complementary text area Enzyme Property Window You can use this window to edit a restriction enzyme Enzyme Name EcoRI a Restriction Site es Normal GIAATTC Complementary The number of bases j6 Kind of Gut Item parameter Description Enzyme Name text area A text area used to enter the name of the restriction enzyme you want to create The OK button is disabled if t
100. the button on the toolbar 2 The following dialog box appears Find BEI Find What 0 Find Way Normal w Direction Down zl Fal nco MENN eo e Help 3 Enter a character string you want to search for in the Find What field 4 Click the Find All button 5 The range of all the matches found is selected They all are colored orange except for the last one which is pink 6 To jump to the next match select the Sequence and then Find Again or press the F3 key The search process is case sensitive uppercase and lowercase characters are distinguished Matches are colored in the Map View so that you can at a glance see the distribution of matches over the entire sequence Selecting Sequences as the Target of Search Normally a search handles the sequence that is currently selected as the target If you want to search within another sequence you must first set that sequence as the target Searching Multiple Sequences You can select multiple sequences within the same project as the target of a search for a sequence string 1 Select Sequence and then Find or click the re J button on the toolbar 2 The following dialog box appears Chapter 2 DNASIS Basics 51 Find Lx FindWhat S Tina Find Way Normal w Direction Down x igel Find Range Current Sequence x I Marker me Help 3 Enter a character string you want to search for in the Find What field 4 Select All Sequences in the
101. the end position 2 A spiral will be drawn Spiral Type beta SLI The operation is described below 1 Click amp on the Toolbar and drag the line that will be the center of the spiral while editing from the start position to the end position 2 A spiral will be drawn Adjust a Figure It is possible to adjust such as rotate reverse normal figures and spirals The following adjustments are possible 278 Create Plasmid Maps Type Before Adjustment After Adjustment Spin left Spin right Spin free Reverse Horizontal Reverse Vertical VV Ui L VA Z Ue Bring to Front Send to Back Bring Forward Send Backward Group Ungroup Change a Figure The size or position of normal figures and spiral can be changed by using the mouse Figures can also be changed by changing the figure properties The operations to change normal figures and spirals are described below Change a Normal Figure By changing the property of a normal figure the thickness and line color can be changed To change the properties of a normal figure select it and click on the Toolbar When the dialog appears enter the items to change Change a Spiral By changing the property of a spiral features such
102. the example If the range to calculate quality is 10 it means that the quality value is calculated every 10bp count Enter a numeric value in the 2 field This value shows a criterion to determine whether or not the quality is low 3 Click the OK button Trimming Unconditional End 1 Click the Vector amp Low Quality Trim End icon and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear ice Trimming Parameter Editor gt M Trim End F 5 END I Trim at least I 10 bp Trim the first 20 bp while the quelity is less than 1 7 EE ey I Trimat least 10 o Sa Trim the first 10 bp while the quality i less thar 90 a I Same as 5 END 2 Enter the bp count of the end to be trimmed in the 1 field in the Parameterset Editor window as shown in the figure 3 Click the OK button to close the dialog box Analyzing the Trimmed Sequence There are two ways to analyze the trimmed sequence Selecting the Trimmed Sequence 1 In the result of analysis for trimming click the bar indicated with Trimmed Sequence A trimmed sequence is now selected as shown in the figure Chapter 3 Details of Analysis 83 ttl ttt TAGTCAGACG TCTTTTTGT CTTCAAATTT TTGTAGGAGL armed Temes w gt ne gt a ABACCATOGC CIACAATTTG GTACTCTOO TOTACGAGCS 2 Click the 2 button on the toolbar 3 The trimmed sequence is now added a
103. the location of amino acid motif databases If the list does not display any registered databases you can click this button to specify where you want your databases stored The Amino Acid Motif Database Directory dialog box appears Help button Displays online help Editing the Contents of a Motif Database In the Amino Acid Motif Database Manager double click which database you want to display contents for The Database Property dialog box appears 240 Databases Database Name PROSITE Release 13 T D Loc of Motifs F Last Modified Date 2001 4 18 Comment SAO OOOO OOOO OOK a SOOO OOK eck PROSITE data file Ek Release 13 0 of November 1995 SAO OOOO CE The patterns section of PROSITE is developed by Amos Bairoch Medical Biochemistry Department CMU The following describes details about this dialog box Item Database Name Description Name of the motif database The database name must not exceed 64 characters It cannot contain double byte characters and these characters that are not supported for file names lt gt D DB Lock Indicates the lock state of the motif database Place a checkmark in this box to lock the database to prevent it from being edited of Motifs Displays the number of motifs stored in the database Last Modified Date Displays the date when the database was edited last Comment Displays comments for the database if an
104. the same position one line below the sequence The cursor Left key Moves the pointer back one character The cursor Right key Advances the pointer by one character The Home key Moves the pointer to the start of the sequence The End key Moves the pointer to the end of the sequence Inserting and Deleting Sequences With the Insertion Pointer flashing you can insert and delete sequences in the following procedures The Character input area Inserts characters that have been entered The Edit and Paste Inserts the content of the Clipboard The Ctrl V key combination Inserts the content of the Clipboard The Del key Deletes the single character to the right of the Insertion pointer The Back Space key Deletes the single character to the left of the Insertion pointer You cannot use any invalid characters as DNA sequences or amino acid sequences For the list of characters you can use refer to Characters You Can Use for DNA Sequences and Characters You Can Use for Amino Acid Sequences in Section 2 2 Any invalid characters as DNA sequences or amino acid sequences will be removed Pasting from the Clipboard Select Edit and then Paste or press the Ctrl V key combination to paste the content of the Clipboard Note however that the operation may vary depending on the working conditions With the Insertion Pointer flashing The content of the Clipboard is inserted as a sequ
105. the selected object Regulation menu Description Spin left Rotates the selected object 90 in a counterclockwise direction Spin right Rotates the selected object 90 in a clockwise direction Spin free Rotates the selected object any given angle Reverse Horizontal Inverts the selected object Reverse Vertical Reverses the selected object Bring to Front Moves the selected object to the front Send to Back Moves the selected object to the back Bring Forward Moves the selected object forward Send Backward Moves the selected object backward Group Groups the selected objects Ungroup Ungroups selected objects Object Normal menu Line Description Draws straight lines Arrow Draws arrows Curve Draws curved lines Rectangle Draws rectangles Ellipse Draws ellipses Polygon Draws polygons 268 Create Plasmid Maps Text Creates text areas Label Creates balloon texts Spiral Type alpha Draws spirals of Spiral Type alpha helix Spiral Type beta Draws spirals of Spiral Type beta helix Object Plasmid menu Add restriction enzyme Description Adds restriction enzymes Insert DNA by enzyme Adds DNA to the positions of the selected restriction enzymes Annotation Adds annotations to plasmid regions Delete Object Deletes selected restriction enzymes DNA or annotations Read file Imports external files Alig
106. using profile icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button Make Multiple Mignmest Profile Parameterset Edtor x x General ParniceAkernent MultipeAlierment ProteinGsp Tree Brotie Nare F Bequerce Type Pretein Output Order Order by Nigred I Use FAST Aleorithen tor the alenant Protein Chars ABCOEFGHIKLNNFORSTUVWYZ DNA Chars ABCOGHENNRS TUVW Cox ee 2 In the Profile Name field enter a file you want to create and then click the OK button 3 In the Sequence View select a sequence you want to analyze a sequence to be added to a tree as the target 4 Click the Phylogenic Tree using profile button in the Analysis menu Explanation of the Result Window When a branch is added to a phylogenic tree created using a profile the branch is shown red For details about the window that displays phylogenic trees refer to the Explanation of the Result Window in Section 23 Phylogenic Tree DNA je lt G4 Q07 BUC a pp O tt Semerentiit4 sil ILI Semarestti 2 184 Swasti Added sequence 164 Details of Analysis 3 43 NCBI Entrez Search Refer to 7 1 3 Initial Setting This function connects the NCBI s Web site and performs entry search based on keywords from the Entrez database It also produces a list of accession numbers and definitions as the result of analysis Selecting a sequence record from this list results
107. when designing a probe Enter regions as follows startbp length startbp length startbp length Example Specifying 50 2 80 5 indicates a 2bp region starting from 50bp and a 5bp region starting from 80bp that is 50 51 bp and 80 84bp You can specify more than one region delimited with a space Hyb Oligo Size Specifies the minimum value Min optimum value Opt and maximum value Max for the designed probe size bp Hyb Oligo Tm Specifies the minimum value Min optimum value Opt and maximum value Max for the Tm value degrees Celsius for the designed probe Hyb Oligo GC Specifies the minimum value Min optimum value Opt and maximum value Max for the GC value for the designed probe Hyb Oligo Self Complementarity Specifies the maximum value for probe self complementarity Hyb Oligo Max 3 Self Complementarity Specifies the maximum value for self complementarity at the 3 end of the probe Max N s Specifies the maximum of number of Ns undefined bases that can be allowed for the probe Hyb Oligo Max Poly X Specifies the maximum number of consecutive identical bases e g AAAAA within the probe Hyb Oligo Min Sequence Quality Specifies the minimum value for the sequence quality within the probe sequence Hyb Oligo Max Mishyb Currently not supported Hyb Oligo Salt Concentration Specifies salt concentration mM used to calculate the Tm value for the probe
108. width No Folding Back Characters alaisi Ee oe pome pe e nsu CES ICE S E ETGEN sag 222 gt 252 Dew at o gt Ome Bowe f One line is used to display without folding back characters to a specified width 1 Click the button on the toolbar 2 Alternatively select View and then Preferences _ In response to a dialog box that then appears set Fold Sequence on the Folding Ruler page to No Fold Using the horizontal scroll bar you can scroll through the part extending past the viewable area of the window Folding Back Characters According to the Window Width With this method the characters to be displayed are folded back according to the width of the window Changing the window size automatically changes the fold back width accordingly alti xy e p oe OF Dsg er antde gt 46 22q 222 ee 222 Schwa gt OMi gem mams 1 Click the J button on the toolbar 2 Alternatively select View and then Preference In response to a dialog box that then set Fold Sequence on the Folding Ruler page to Fold by window width In the block based display mode the number of fold back characters is changed according to a multiple of the block length Otherwise the number of fold back characters is changed on a character basis Chapter 2 DNASIS Basics 37 Folding Back Characters According to a Specified Width With this method the characters to be displayed are folded back a
109. window 2 Click the Create Multiple Alignment Profile button and an Analysis dialog box Then click the Parameter button Profle Nane S Frotib Nanseer Sequence Type Protein Output Order Order by Aligrad I Live FAST Aleorithen dor the alien mart Protein Chars ABCUEFGHIKLNNPORS TLV Wxva DNA Chars ABCOGHEMMAS TLV Ww Y Defouk co e 3 In the Profile Name field enter a profile you want to create and click the OK button To create a new profile select Profile Manager and use the Profile Manager 4 Click the Create Multiple Alignment Profile button DNASIS MAX uses all sequences displayed in the Sequence View to perform multiple alignment and then writes the result into the profile Note Because the profile is overwritten be sure to make the profile setting before pressing the Analysis button Locking the profile prevents an unexpected overwrite Use the Profile Manager for locking the profile Using a Created Profile on Another PC You can export a newly created profile and save it to a file You can also import such an exported profile to use it on another PC The procedures are the same as those for DNA Chapter 3 Details of Analysis 163 3 42 Using Phylogenic Tree Profiles Amino Acid This function creates a phylogenic tree by adding a single sequence to a multiple alignment profile that has been produced in advance Analysis Procedure 1 Click the Phylogenetic Tree
110. you can click the Property button to edit data for a proteolytic enzyme Clicking the Property button causes the Enzyme Property dialog box to appear Enter data in this dialog box to edit enzyme data You cannot change the name of an enzyme to the same name as that of any other registered enzyme Chapter 5 Databases 259 Enzyme Name Comment Acrosin ooe Acros in Recognition Sequence fIKRIX Enzyme Property dialog box Item parameter Enzyme Name NAME Description Enter the name of the proteolytic enzyme The OK button is disabled if this field is blank Recognition Sequence SITE Sequence recognized by the proteolytic enzyme An amino acid sequence is represented in the single character format with an exclamation mark indicating a cut position If there is more than one recognition sequence a slash is used as a delimiter If there is more than one recognition amino acid complex code the acids are enclosed by brackets X indicates any amino acid Example KR X AR X Identify KX RX and ARX and cut between K and X R and X and AR and X The OK button is disabled in the following cases For each sequence separated by a slash 1 There are more than one cut position 2 The data does not contain any amino acid characters 3 Any character other than A to Z and is used 4 Brackets are nested in other brackets 5 Brackets are not paired
111. 0 00 8 00 jacoocctecttttctaagca Right 2758 2778 20 60 428 5 000 4 00 0 00 jececctataaccacet tec Product 2671 2775 208 I i ecccoctcocttttctasecaecateaatsagcateatereeacttae Pair 3 00 1 00 2 ow 4 2 Click any of the check boxes on the left to uncheck a primer you do not want to display 3 Click the OK button Changing the Tm Value for a Primer to be Designed 1 Click the Primer Design icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear 2 Select the Primer Picking Conditions tab in the Parameterset Editor window as shown in the figure PrimerParameterEditor x Penalty Weights for Primer Hyb Oligo Conditions Penalty Weights for Hyb Oligo General Parameters Primer Picking Conditions Pre Sequence Inputs Primer Size Min 18 Opt Max 27 Primer Tm Min 57 Max Tm Difference Product Tm Min TAT Primer GC Min 20 0 Max Self Complementarity fe Max N s Inside Target Penalty First Base Index if Salt Concentration 50 M Liberal Base fo Opt feo Max e3 7 Opt Max Opt Max e00 Max 3 Self Complementarity 3 Max Polyx 5 Outside Target Penalty fo CG Clamp fo Annealing Oligo Concentration 50 Default 90 Details of Analysis 3 Set the following values in the Primer Tm field Min The minimum Tm value for the primer to be designe
112. 0 Sequence CGACTTCCTC TTTC Annotation Experimental Sequence TTTCTCGAAA AATGAGCCAA Annotation Experimental Sequence TIGCTCTT Annotation Experimental Sequence TGTCAA TAGGATGANC CTAAGCTTGG GTCTCCCTAT AAGTTAAGTN GNATTA Annotation Experimental 2 Select Sequence and then New DNA or press the 2 button on the toolbar 3 Asequence whose name begins with Untitled001 is added to the end of the sequence list The sequence corresponding to the ranges selected in step 1 is duplicated by joining them from left to right as shown in the figure Sequence TGTNAGGTCN NNAGGGCGNG NTNNTGTGGN Annotation Experimental Sequence NCNTNNTGTG GI 0 130 Sequence G G AATGTTTCAT CGCATTTTGG AAGAACTT Annotation Experimental Sequence Sequence TTTCTCGAAA AATGAGCCAA Annotation Experimental Untitled002 Sequence Itrace sct Sequence Annotation Sequence 4 If different sequence range is found duplicated or nothing is found duplicated make sure that the regions of the sequence which are to be duplicated have actually been range selected as the target Duplicating the Sequences Entirely You can duplicate the sequence entirely 1 Select a sequence you want to duplicate as the target 2 Select Sequence and then Duplicate 3 All of the sequence selected in step 1 is duplicated under the Original sequence name Copy name at the end of the sequence list The original sequence and
113. 3 ATGTGCAGOGOTOGCA 1538648 ATGATGCAGGACCAGC 1525529 ATGCAGGACCAGOTGG 14550 27 ATGAACGGCOGCTTOTO 1314007 ATGGAGOOCATGCACC 1278364 ATGCACCGCTACGACG 1121799 ATGACCAGCTCGCAGA JAAAAAAAAAAAAAAR A RE You can copy and save the ORF list The data that has been copied or saved can be used by other applications such as MS Excel Click to display a list of Start Codons and Stop Codons not in the reading frames Selecting an ORF to Display 1 Follow the procedure in the previous operation to display the ORF List window 2 Click the checkboxes of the ORFs you do not want to display in the list to uncheck them Immediately after analysis the start and stop codons outside the reading frame are not displayed in the Map View However you can display them by placing a checkmark on this list 3 Click the OK button Narrowing Down the ORFs to Display 1 In the Sequence View double click in the result of searching for ORFs Alternatively you can right click an ORF in the Sequence View to select the Show Setting menu 86 Details of Analysis 2 Select the frames you want to display from the Frame field Those frames with the checkmarks placed in the checkbox are displayed Note If you select the All Frame field all ORFs are displayed in a single frame 3 Select the length of an ORF you want to display from the ORF field Frame VV Frame 1 M Frame 1 T All Frame MV Frame 2 M Frame 2 VV Frame 3 M Frame 3 OR
114. 5 Original Sequence 39 42 P Phylogenic Tree 121 130 162 165 209 215 PIR Format 26 Plasmid 266 Preferences 11 Primer Design 89 187 Print 56 282 Profile 127 130 164 165 210 215 Project 57 Proteolytic Enzyme 259 Proteolytic Site 155 223 R Restriction Enzyme 194 245 Restriction Site 95 Reverse Complement Sequence 70 177 Reverse Sequence 71 178 Ruler 37 S SCF Format 26 27 Search 51 95 99 102 110 114 116 135 145 149 155 157 158 159 166 169 196 197 201 202 203 218 223 264 288 294 Secondary Structure 143 222 Selecting Sequence 49 51 Sequence Database 229 Sequence Name 28 Sequence View 3 56 Smith Waterman Search 116 159 203 Stacking Site Search 199 302 Index Start Codon 86 Switch Pane Toolbar 5 T Tandem Repeat Search 200 Target 49 Tm 90 Toolbar 5 Trace 26 61 Translation 72 179 Trimming 81 183 299 Tutorial 285 V Vector 81 183 234 299 W Waveform Display Mode 58 Index 303
115. 7 cgc gt cgg R 3 EcoH 428 432 gcggg 428 lccsgg 427 ccc gt eeg P 3 EcoHi 599 603 accgg 599 lccsgg 598 atc gt ata 1 EcoH 651 655 gccgg 651 lccsgg 650 ctc gt ctg L 3 EcoHi 698 702 tess 698 ccses 697 zgc gt gst G 2 EcoH 709 713 gccgg 709 lccsgg 708 gcc gt gcg A 2 EcoH 721 725 gcggg 71l lccsgg aE 720 gcc gt gcg A 3 EcoH 1079 1083 tecgg 1079 loesgg 1078 ecc gt ect P 1 EcoH 1119 1123 gccgg 1119 lccsgg 1118 gtc gt gtg V 1 EcoH 1227 1231 gocgg 1227 lccsgg 1226 ggc gt ggg G al ASSRRANELE a Stn Codon Table name Codon table name used Frame No Frame number Enzyme NAME Name of the restriction enzyme Find Position Position of the restriction enzyme searched for Mutation Seq Sequence of the mutation site MUT Pos Position of the mutation Recognize Seq Recognition sequence for the restriction enzyme CUT Pos Position to cut Translation Change in translation by the mutation site Selecting a Codon Table 1 Click the Mutation Site Search icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button 2 Select a codon table you want to change from the Codon Table field in the Mutation Site Parameter Editor window as shown in the figure 102 Details of Analysis Godon Table Universal Z Output as HTML format Check All cronuclear Uncheck AIl ate Mitochondrial Mo
116. 70 Sequence SNLSHMGPSY DLOTFSLHLA GISSILG 41 NFITTIISMR WEGMOMERLP LFYWSSI Sequence SNUSHWGPSY DUSIFSUHLS GISSILGG41 NFITTIISMR an00002 2736p 04 Sequence SNUSHHGPSY DUSIFSLHLA GISSILGGAI NFITTIISMR Wee TTS Sequence SNUOHHGPSY DLAIFSLHLA GISSTLGGAI NFITTIISMR WEGMOMEELP LFYWS 190 200 210 220 Sequence WLLLLSLPYL AGAITMLLTD RNFNTTFFDP SGGGDPILYQ HLF Sequence YLLLLSLPYL AGAITMLLTD RNFNTTFFDP SGGGDPILYQ H 2 On the View Toolbar click the Alignment icon to cancel the alignment display mode Now you can move on to analysis 3 Start the analysis Because the range selected in step 1 above is interlocked here it gives a rough measure of the region of analysis Creating a Consensus Sequence Based on the result of alignment the most frequently occurring amino acid is selected as the consensus for each position From menu bar in the Alignment Mode Window Select Sequence and then Make Consensus The consensus sequence is added to the Sequence View Chapter 3 m0001 m0002 m0003 m0004 Untitled001 m0001 m0002 m0003 m0004 Untitled001 Sequence Sequence Sequence Sequence Consensus Sequence Sequence Sequence Sequence Consensus Sequence Sequence TRCCCECCEE TAAATGGGG CGACACTCCG CCATGAATCA CTCCCCTETG AG GCCAGCCCC CTGATGGGGG CGACACTCCA CCATAGATCA CTCCCCTETG AG GCCAGCCCC CTGATGGGRG CGACACTCCA CCATGAATCA CTCCCCTETG AG GCCAGCCCE CTGATGGGGG CGACACTCCA CCATGAATCA CTCCCCTETG AG TGCCAGCCCC CTGATGGG
117. 9 60 000 4 00 0 00 occctateaccacstttcca Product 25701 2774 205 caccocct ct tt ictaascascatgaataagcateateceeactte Pair I 3 00 1 00 3 Left 2569 2588 20 59 927 55 000 3 00 3 00 ccaccecctecttttctaas Right 2755 2774 20 59 679 50 000 4 00 0 00 ccectataaccacetttcca Product 2569 2774 206 coacccectocttttctaagcagcatgaatasgcateateceeactt Pair 3 00 0 00 4 Left 1631 1650 20 69 993 45 000 3 00 0 00 jaetctocaseceaceaaaaa Right 1793 1818 20 59 911 50 000 6 00 2 00 jecacetttecaactetecta Product 1631 1818 188 agtctccaagceacgaaaaaaaatettttaatatttecasecaactt Pair 5 00 0 00 5 Left 2571 2530 20 60 068 50 000 3 00 3 00 accecctocttttctaasca Right 2756 2776 20 60 423 55 000 4 00 0 00 jccccctataaccacetttoc Product 2571 2775 205 acccoctoctttictaagcazcatesatsazcal eat eezeacttae Pair 3 00 1 00 i feces ECT Selecting the Primer That Amplifies a Selected Range If you know the region you want to amplify in a sequence in advance you can design the primer to always include this region in the PCR product 1 In the Sequence View select a portion you want to amplify 2 In the Analysis Button View click Primer Design Sequence View Result of Primer Design If you double click the primer its detail is displayed in Chapter 3 ee mt Details of Analysis 89 Range to be amplified Primer that amplifies a selected range Selecting a Primer to Display 1 In the Sequ
118. A TACACOCGM ACAATASCHG CATICTOCTC PETCAOCCAC ATCTEOO Gretar costrenn atroitats TOCATOCAL Coomoctca avatrer A7GTsksTTA COACTGAATC ATTOGETATA TeCATOCAss COGUANCTCA aTATTCT Memoria Tatecatets GhaCeManet TaTacTaGey aToCTaTacT TiTcTas 7 3 7 Adding Annotations to Similarities A yellow background is shown on the portion having a match between two sequences Below we ll demonstrate how to add an annotation to the area of high homology in the 301bp to 540bp range in this example First select the range from 301bp to 540bp using the mouse Chapter 7 Tutorial 295 8 8 3 8 35 2222 vouszea 4 paed s gt FERTELT This displays the dialog box where you can add annotations Enter Homology with M98484AALMTCYTOB as the annotation name and click the OK button As a result an annotation with the Homology with M98484AALMTCYTOB name is added woua ES a C S oae saie f CEJ e m T ELTE SRB ir eee Sse Stet ive pesemas ne 296 Tutorial Chapter 7 Tutorial 297 7 4 Vector Trimming Vector trimming is used to find the vector sequence part from the output data of an automated DNA sequencer Vector sequence can then be masked You can also load a reference sequence and align it with the sequence based on the data from your sequencer and display the two aligned sequences and the waveform data from your sequencer simultaneously e Waveform display e Vector trimming
119. A drop down list which helps you specify a motif pattern You cannot use this list if the database is locked The available items include Enters a caret character at the beginning of a sequence Enters a period which matches any character Enters a dollar sign at the end of a sequence Enters a vertical bar which means or Enters parentheses for grouping Enters brackets which means a range of characters Enters a caret and a space within brackets which means characters other than those in the specified range Enters an asterisk which indicates zero or more repetitions Enters a plus sign which indicates one or more repetitions Enters a question mark which indicates zero or one repetition Enters braces which means n repetitions 256 Databases Item Match at least n times Description Enters a comma which means n or more repetitions Motif Pattern Test Sequence Enters a sequence used to test the pattern Clicking the Test button causes any section that matches the pattern to be highlighted Test button This button is used with the Motif Pattern and Motif Pattern Test Sequence fields to test the pattern Clicking the Test button causes any section that matches the Test Sequence pattern to be highlighted If more than one section matches only the first match is highlighted This button is disabled if the Motif Pattern or Motif Pattern Test Sequence is
120. AANNINNTTG GIGTACG NINNGTC GACNINNGTG Goals GIGNGC OCISGG Item parameter Name 5 extended 5 extended 5 extended 5 extended 5 extended 5 extended blunt cut Delete Property Import 5 extended 3 extended 5 extended 5 extended tt Description Name of the restriction enzyme Recognition Sequence Indicates the sequence that the restriction enzyme recognizes in the direction from 5 to 3 An exclamation mark indicates the position to cut If the recognition sequence does not have a palindrome structure the sequence recognized by a Normal sequence and that recognized by a Complementary sequence are separated with a slash Bases Indicates the number of bases in the recognition sequence Kind Of Cut Kind Of Cut Indicates the shape of the cut performed by the restriction enzyme 5 extended Cuts the sequence so that the 5 end is longer than the 3 end 5 GIAATTC 3 3 C TTAA G 5S 3 extended Cuts the sequence so that the 3 end is longer than the 5 end 5 TGCGICA 3 3 ACGCGT S blunt cut Cuts the sequence so that the 3 and 5 ends have the same length not identified 5 CCCIGGG 3 3 GGGCCC S Indicates that you cannot identify the position to cut for this restriction enzyme If you check this enzyme it will not be registered as a parameter 244 Databases Button Description New button Creates a new restriction enzyme The New Enzy
121. ANY IMPLIED WARRANTIES ARE LIMITED IN DURATION TO NINETY 90 DAYS FROM THE DATE OF DELIVERY OF THE SOFTWARE THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS YOU MAY HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE LIMITATIONS OF REMEDIES Mirai s entire liability to you and your exclusive remedy shall be the replacement of the Software media or the refund of your purchase price as set forth above If Mirai or the Mirai s distributors are unable to deliver replacement media which is free of defects in materials and workmanship you may terminate this Agreement by returning the Software and your money will be refunded REGARDLESS OF WHETHER ANY REMEDY SET FORTH HEREIN FAILS ITS ESSENTIAL PURPOSE IN NO EVENT WILL MIRAI BE LIABLE TO YOU FOR ANY DAMAGES INCLUDING ANY LOST PROFITS LOST DATA OR OTHER INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY OF SUCH DAMAGES OR FOR ANY CLAIM BY ANY OTHER PARTY SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION OR LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES TO THE ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO YOU GOVERNMENT LICENSEE RESTRICTED RIGHTS LEGEND If you are acquiring the Software on behalf of any unit or agency of the United States Government the following provisions apply License Agreement iii The Government acknowledges Mirai s representation that the Software and its documentation were developed at private expense and no part of them is in the public domain
122. ATOTOCAGOGOTOOCA Iaa ATOATOOAOGAOCAN IS ATOAGA TOR 102 ATOMOQOOCOOTTOT IMAG ATOCAGOOCATOCAD 17764 ATOCAODGCTAOGACR 1ITI1298_ ATRANOASOTOROAGA CJ _ coe BORLAAAATARLeSsHsse To save the ORF list select Export from File in the menu The list will be stored in a text file containing the information separated by tabs 290 Tutorial 7 2 6 Entering the Amino Acid Sequence for Selected ORFs into the Editor Clicking the longest ORF in the Sequence View causes the amino acid sequence of the corresponding frame to be highlighted In our example the amino acid sequence in the first reading frame is highlighted ELEZE TEELT sr 8 ee SS peen ors oot sd S a cc bam eea Orte SSDP eote DOUT ere lt aeaee eaaa aee aeae ou Seema nate tS tei 1 a he i wa 4 Click the Amino Acid Transfer DH button This moves you to the amino acid editing mode in which the translated amino acid sequence is entered into the Editor D p po m e M SBF CRAB 48 BIB tee L ver sze0 pusxas Di Du Aamo men mem marar wane ame oi w If You Want to View the Result of ORF Search When a new amino acid sequence is created the edit mode switches from DNA sequence to amino acid sequence Viewing the analysis result for DNA sequences requires you to go back to the nucleic acid sequence mode To do this click the DNA Mode button Zp Click the Amino Acid Mode button EA if you want to edit
123. Acid Basic _ Rename AminoAcid Searc A Parameter Aminodcid Comp Analysis Dialog eT C E ran 2 An icon is duplicated just below the button and the button name is ready for editing Change the button name to something else 3 Click the duplicated icon and an Analysis dialog will appear Then click the Parameter button 4 When the parameter setting dialog box appears change all parameters 5 Click the OK button to close the dialog box Changing Analysis Names in display In column 2 of the Sequence View the analysis name is displayed to the left of each result of analysis By default the name of the analysis button used to perform the analysis is set here You can manually change the displayed analysis name in the following way 1 In the Sequence View click an analysis name you want to change The particular name then becomes the target which is now underlined 2 Click the name again 3 After a 0 5 second delay the outer frame is displayed in which you can perform editing trace scf Sequence GTTCCA 4 After editing press Enter or click somewhere outside the frame Renaming Analysis Buttons You can change the analysis name associated with the button Right click an analysis button you want to duplicate 1 From the menu select Rename 2 Since the button name is now ready for editing as shown in the figure change the button name 3 After editing press Enter Chapter 2 DNASIS Basics 45
124. Auternation Contig Manage Sequence aattcotggg acttgggeag gtatctgtge tgcagaggtt ttagaaagte Azsotation soure t ooure jendindex Homology Seach ta pre Ra CDS Sequens ttgtaacgtg cctttaattt ttesctetgt gcoagcgats gcogcagens Arsotation pource source id pm W CDS Target AF087301 Postion 1 bp Comment Conduct Homology Search in Genelndex Launch parameter editor to change species J7 Execute analysis without showing this dialog 4 A browser will open and connect you to the GeneIndex site A database selection page will appear Select target databases for the GeneIndex Homology Search and click Next 5 A page for entering search conditions will appear For the sequence string the sequence shown in DNASIS MAX will display here in FASTA format Enter any other conditions and click Search The search results will appear 6 An Export to DNASIS button will appear in the Search Result window so click it and a DNASIS Export window will appear 7 Set the export parameter and click the Export to DNASIS button again to start the download Upper Limit of Characters In Homology Search the maximum number of searchable characters after converting to FASTA format is 20 000 Each sequence consists of gt at the head title and sequence itself followed by a linefeed That is five characters are automatically added to a sequence Even for multiple sequences the total maximum l
125. BLAST search translation DB tblastx Amino acid BLAST search blastp Amino acid BLAST search translation DB tblastn Detail Displays the Detail dialog box Expectation value E_VALUE Specifies an expectation value DNASIS MAX will only report hits having an expectation value equal to or lower than the value specified here Filter query sequence FILTER Specifies whether the same sequence as the input sequence will be excluded from the search target during database search To exclude the same sequence select this check box Include gap in alignment INSERT_GAP Specifies whether to include a gap in alignment Descriptions Descriptions DNASIS MAX to output up to a specified number of entries if the search results contain a large number of entries Alignments Alignments Instructs DNASIS MAX to output up to a specified number of alignments if the search results contain a large number of alignments Nucleotide Database Amino Acid Database Target Databases Displays nucleic acid or amino acid databases depending on the type of the program Select the check boxes of the databases you want to search Select All Selects the check boxes of all databases Deselect All Clears the check boxes of all databases Setting Opens the BLAST Database Manager dialog box You can change the directory in which DNASIS MAX will store the databases Default Resets the parameters to their initia
126. Chars ABCOEFGHIELNNPORS TLV WiYZ DNA Chars pa DOHIMNRSTUVN Y 2 In the Profile Name field select a file you want to create and then click the OK button 3 In the Sequence View select a sequence you want to analyze a sequence to be added to a tree as the target 4 Click the Phylogenic Tree using profile button in the Analysis menu Explanation of the Result Window When a branch is added to a phylogenic tree created using a profile the branch is shown red For details about the window that displays phylogenic trees refer to Explanation of the Result Window in 3 23 Phylogenic Tree DNA t au lIe lt EA QQOM gt BH gt C4 o 0 002 0 05 Seauencet004 0 008 eart aori 747 008 Seauencet021 0 00416 004 Seauence026 0 006 Sequence0015 008726 poe oe 0 014 Sequence018 0 000 0 018 Sequence029 0 021 _____Seauenee0005 0 020 el oon Sequence0010 0 91 guence0006 mai 0 042 Seauence0012 0 001 o 01 Sequence002 01 0 023 p ee Sequence0022 9 0033 19 010 Sequence0025 0 006 Sequenced001 4 002 601015370008 Seauencet008 0 001 aaa a 0 092 Sequence027 a oti Sequence0003 0 000 0 020 Sequence0020 U 001 fy Sequi 0 008 6 g 0 032 0 030 Sequencel023 0 0022nce0000 0 006 Seauenced0 14 0 108 Bett 3 0 015 Sequencell028 000k 0 030 Seque ee0008 N A a 0 021 Sequence019 a 1
127. Clustal W Selecting the check box enables the parameter Note Initially a positive matrix is used If this parameter is selected a negative matrix is used Chapter 4 Protein Gap Details of Parameters 211 Make Multiple ignenent Profile Parameterset Editor cam xj General PaiwiceAlienment NultioleAliennent Protein ap Tree l Repre ace off I Excrophile cape off Hydrophilic Residues Gap Separation Distance 100 I End Gap Separation IGPSNDOEKR 0 Item Residue Specific gap off Corcel Help Description Corresponds to the nopgap parameter of Clustal W Selecting the check box enables the parameter Note Specify GapPenalty for each amino acid A gap is likely to be inserted where many amino acids are set in the sequence data Hydrophilic gap off Corresponds to the nohgap parameter of Clustal W Selecting the check box enables the parameter Note Specifying this parameter increases the probability that a gap is inserted if five or more hydrophilic amino acids are contained consecutively Hydrophilic Residues Corresponds to the hgapresidues parameter of Clustal W Note Specifying this parameter reduces the probability that a gap is inserted if gaps are too close to each other A penalty is given if gaps are closer to each other than the value specified here Gap Separation Distance Corresponds to the gapdist parameter of Clustal W End Gap Separation Corresponds to the endga
128. Complementary sequences Button Description Check All button Selects all the checkboxes for the motif databases Uncheck All button Unselects all the checkboxes for the motif databases Setting button Starts the Nucleic Acid Motif Search Database Manager for setting database directories Default button Returns parameters to default values aramEditor Details of Parameters 195 4 14 Mutational Site Search Codon Table Universal z Output as HTML format Check All Restriction Enzyme List Uncheck All Kndct Ot check Selected ee Aar CACCTGC GCAGGTG fost AatI AGGICCT ECA es AatIl aacaTc ITECA fos Aaul TIGTACA ECA DOS Acct 131 AGTIACT fee Aco 61 TGCIGCA tee ACCS ACCTGCNNNN NNNN NNNNNNNNGCAGGT 5 extended tee Acc 5I GIGTACG D8 Acct GIGYRCC Dee AccB71 Oin AccBSI DOME AccI GTMKAC O Accll Restriction Enzyme Database Manager Item Enzyme Name NAME CCANNNNINTGG CCGICTC GAGICGG not identified blunt cut Uncheck Selected 3 extended 5 extended Show All blunt cut blunt cut Show Selected 5 extended Show Checked 5 extended 3 extended Show Unchecked blunt cut 5 extended blunt cut Description Name of the restriction enzyme DNASIS analyzes the cut region using the restriction enzyme selected with the check box on the left Recognition Sequence SITE_N SITE_C Indicates the sequence that the restriction enzyme recognizes in the direction from 5 to
129. Conditions Penalty Weights for Hyb Oligo l General Parameters Primer Picking Conditions Pre Sequence Inputs Included Region Start Codon Position r Sequence Quality Min Sequence Quallity fo Sequence Quality Range Min 0 Min End Sequence Quality fo Sequence Quality Range Max 100 Default 3 Click the OK button 94 Details of Analysis 3 13 Restriction Site Search This function searches DNA sequences for recognition and cutting sites of restriction enzymes and displays the result of search Explanation of the Result Window Mi Foew ction Eny me Position cut by the e ee ose er enters restriction enzyme 7 ERLA E L 5 T Sequence View Part of recoanizina the restiction enzyme etassececes tccceezese Caeacaseec catttcecct segeccestc etctettcce i Selected Alwl Amab7l restriction Avot Restriction enzvme of the same type as the selected one Map View The pin shows the position where the restriction enzyme cuts If you move the cursor to the pin and click it the You can display color changes and the pin is selected If there is more than one position to cut by the same restriction change the enzyme all of them are highlighted display color Refer to 1 5 A Sequence View Preferences Dialog Box Together with the sequence the following are displayed the name of restriction enzyme the part of recognition and the position to cut If you click the mouse the p
130. DNA Toolbar Views hides the DNA toolbar Amino Acid Toolbar Views hides the Amino Acid toolbar Annotation Toolbar Views hides the Annotation toolbar Status Bar Views hides the Status Bar Preferences Displays the Preferences Internet Options Displays the Internet Setting dialog box Help menu Contents Function description Displays online help User Forum Web Page Displays a Web site for the User Forum of DNASIS MAX This requires an environment capable of being connected to the Internet About DNASIS MAX Displays the version information Popup Menu on Annotation Display Menu Selected Annotation Setting Description Displays the Annotation Setting dialog to set the parameters for the selected annotation or part Annotation List Displays the Annotation List dialog to list up annotations Kind Color Setting Displays the Kind Color Setting dialog to set colors New Annotation Create a new annotation Add Annotation To Selected Adds the selected range as an annotation Area Add Annotations To Selected Adds a selected area and an emphasized area as separate annotations And Emphasized Area Add Annotation Parts To Adds annotations that have selected areas and emphasized areas as separate annotation parts Selected And Emphasized Area Duplicate Annotation Duplicates a selected annotation
131. Deletes the database Update Immediately updates the database Actually DNASIS re creates a database by converting all entries of the source sequence data Set schedule With a database selected clicking this button sets an update schedule Clear schedule Clears the update schedule settings DB Path Allows you to specify the path of the directory to store the dedicated database for BLAST searches Scheduled Update Entering a date and time and checking this check box causes DNASIS to automatically update the database on the specified date and time You can press the Delete key in the date field to clean the field In that case DNASIS will update the database every day at the specified time However you cannot use that function for a dedicated database for BLAST searches Help Displays online help Close Closes the BLAST DB Manager Chapter 5 Databases 263 Select Sequence Database dialog box In the Sequence DB Manager select the data you want to convert and click Make DNASIS registers the selected data with the BLAST DB Manager In the BLAST DB Manager clicking the New button causes the following dialog box to appear 56 209 1998 8 4 bacterial sequences INV 10 023 1996 11 27 invertebrate sequences P MAM 18 054 1998 3 16 other mammalian sequences 2 PAT 131 845 1993 1 28 patent sequences PHG 1413 1986 7 2 bacteriophage sequences amp PLN 43712 1998 12 22 plant fungal and alga
132. E aay unin ta asbeun caves aabeuree este tus E 130 3 28 Clustering seas cevasuis isansenadeedsatssutncisasasdatatudnaets sate vedas daceaawasdhwas SudbaraauceieWaseetuastayinsavvadsesashansvoueas 131 Explanation of the Result Window ccccescsscssseseesscseceseeseeseesecsececeaeeaeesecaeeeeeeeeaecaeeaecaeceeceeeeaeeaeeaeeneens 131 Setting the Clustering Standard iis s cesciscescsadcesscssscessadaccssecesecensesaces sexes aces earar Sar E raris ROSEE VERS EEs 132 3 29 BLAST Search and Extraction Report cccccsssesccesseeeeeesneeeeeesneesesesneeseeeseeeseeesneeseeeeees 134 Explanation of the Result Window 22 cccthsssdestccgevsace geasedete tears ERE ER E E REES 134 Specifying a Database to Be Searched cee E ARER REEERE TENORE 135 Settmg Extract Comditrons assises eier rah o aE EA oE REE TE EE REE ORA EEA Rh ri 136 3 30 Amino Acid Contents s osien sninen inaina prane aea anaE E aaas P nanmi erens e aiaa ARE in anra Ra ASTREA nR RE AE Explanation of the Result Window 3 31 Isoelectric Points Explanation of the Result Window 3 32 Hydrophilicity Hydrophobicity and Secondary Structure cccccesseeceeeseeeeeeeseeneeeeees 141 Explanation of the Result Windowns erea AEN E E RN a A 141 Selecting d Tablete a err SE EEN EE EEEE EARE EREE EEEE OA E EAE AEE A E ERE 141 Creating and Editing a New Table ccc sssssacssvesscozansceasadascavssaveceased sdeassssnecesdedadeasssssoasbacadecasssnesevsaiaiezesasaaie 142 3
133. ESE Perameterset Type HSK_DNASIS_Assenble Parameters Min Overlptencth 0 M Mn Match Rate P0 Jf Homokey Compre NA 4 MacMatch Compare NA 200 Jf Cont Heads Cone J TH Ce a Item Parameterset Name Description Display the parameterset name Parameterset Type Display the type of parameterset Parameters Mir Overlap Length Min Match Rate Homology Compare NA MaxMatch Compare NA Contig Header Display the parameters Minimum overlap length to assemble sequences Overlap areas with shorter length than it are ignored Range 1 1000bp The length shorter than Homology Compare_NA is not allowed Minimum matching rate to assemble sequences Sequences with lower rate than it are not assembled Range 100 Minimum BPs compared in homology search Homology search is conducted from to the site with perfect match in the longer bases than it Range 6bp Maximum BPs compared If the length of compared bases is longer than it the length is divided by 2 and compared again Range 200 500bp Contig Name Header Contig name is Contig Name Header making number Character Range 1 59 Valid Characters Alphabet Upper and Lower case and _ Chapter 4 4 26 Clustering Details of Parameters 215 Sequence Clustering Parameterset Editor E E Sequence Type Nucleotides AminoAcid Clustering Mode gt Clustering only Fou sequences each other C Clustering with
134. F IV Show Top fi ORFs in leneth 1 bp r Other M Nested ORF Show Comment Show FrameNo 1 Specify the number of ORFs you want to display starting with the longest one 2 Specifies the length of the shortest ORF you want to display If you place checkmarks in both 1 and 2 only the ORFs that meet both conditions are displayed 4 Sets the following in the Other field Nested ORF Forcibly draws the starting point if nested ORF is displayed Show Comments Displays the comments for the ORF in the Sequence View Show FrameNo Displays the frame numbers in the Sequence View 5 Click the OK button Adding a Selected ORF Sequence to the Editor 1 In the Sequence View or Map View click an ORF to select it 2 Click the 2 button on the toolbar with the ORF selected 3 DNA sequence for the selected ORF is now added in the Sequence View so that you can continue to analyze DNA sequence of the ORF Adding a Comment to a Selected ORF 1 Double click an ORF to which you want to add a comment The ORF Shape Setting window appears as shown in the figure ORF Shape Setting Color Si IV Show ORF Start Bar JV Show ORF End Arrow Width 3 Comment OK Cancel 2 Enter a comment you want to display in the Comment field 3 Click the OK button A comment appears under the ORF as shown in the figure 2770 2 780 2 790 280 etegttata gggggaaatg atgcttcttg tataggaata Chapter 3 De
135. FAST Approximate alignments Protem DNA Gap Peewlty 0 500 j E K tuple word size Froteini 2 DWAT 4 gt EEE me No of top diagonalt 1 50 m TEE Widow see 0 50 TE E Item Gap Open Penalty Carcel Help Description Corresponds to the pwgapopen parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter determines the probability of a gap being inserted A larger value makes it more difficult to insert a gap Gap Extension Penalty Corresponds to the pwgapext parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter determines the probability of a gap being extended A larger value results in a shorter gap Protein Weight Matrix Corresponds to the pwmatrix parameter of Clustal W You can select BLOSUM 30 PAM 350 Gonnet 250 or Identity matrix which sets the value blosum pam gonnet or id respectively Alternatively you can select User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating similarity among amino acid molecules DNA Weight Matrix Corresponds to the pwdnamatrix parameter of Clustal W You can select UB or CLUSTALW 1 6 which sets the value iub or clustalw respectively Alternatively you can select
136. GG CGACACTCCA CCATGAATCA CTCCCCTGTG Aq L L n n GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTACA Gq GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA Gq GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA Gq GTICTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA Gq GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA Gq 130 150 170 CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GA CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GA Details of Analysis 159 160 Details of Analysis 3 40 Phylogenic Tree Amino Acid This function calculates the phylogenic tree by using an input of three or more amino acid sequences and displays the result of calculation Explanation of the Result Window Refer to the Explanation of the Result Window in Section 23 Phylogenic Tree DNA Changing the Type of a Phylogenic Tree You can select a phylogenic tree from four types Phylogram Slanted cladogram Rectangular cladogram and Unrooted From the Tree View toolbar select any type you want to display 023 Sequencet000 69 0 123 equencell0 1 Changing the Font 1 Select View Preferences from the menu bar to display Parameter Set Editor Parameterset Name JHSkK_D NASIS Parameterset Type JHSK_M ultipleAlignmentT reeViewS r Parameters ViewType fo a ShowBarscale false true ShowLeaf false tue ShowLenath false true ShowBootstrap false tue D
137. I Entrez button then select the OK button Entrez Search Search ee Fields Seach 9365066 documents are found 1 1000 are displayed Accession Defestion Tt yi 1 Item Search Key Display Textbox arenbeane 4 supertars member 10 mRNA CONA che AIMO NANA cDNA cions Mi Tok JNA clone IMAGE SEGE B complete odi b relted sblamily memb w Chee Description If the search is successful the search key will appear Comment Display Box If the search is successful the number of hits will appear If the number of hits and the display number do not match number of hits exceeds the number specified in the parameter or no invalid search results appear both numbers will appear If the search is not successful a message No Result will appear Search Result List If the search is successful a list of search results will appear The three display items are Hit Number with icon Accession and Definition It is possible to sort the list with any of the three items as a key It is also possible to select multiple items If the search is not successful nothing will appear in the list Search button Click the button to start the Entrez Search Parameter dialog and perform a search When the search is finished the Search Key display textbox Comment box and Search Result list will be updated Import button Imports the item GenBank report selected in the Search
138. Length Specifies the loop length If the loop length is within the range specified here the loop length will become a hairpin loop region candidate Input range 2 to 99 Input range 0 to 2 147 483 646 Matching Percentage Specifies the match rate within a stem If the match rate is above this specified rate the stem will become a hairpin loop region candidate Input range 1 to 100 Default button Returns parameters to default values OK button Closes the dialog after the parameters have been set with the values entered in the dialog Cancel button Closes the dialog without updating the parameters Chapter 4 4 16 Stacking Site Search Stacking Length 3 10 te Matching Percentage more than 100 Details of Parameters 197 Detautt __OK_ Gancel Item Stacking Length Description Specifies the stacking site length If the stacking site length is within the range specified here the stacking site will become a hairpin loop region candidate Input range 2 to 99 Matching Percentage Specifies the match rate within a stacking site If the match rate is above this specified rate the stacking site will become a hairpin loop region candidate Input range 1 to 100 Default button Returns parameters to default values OK button Closes the dialog after the parameters have been set with the values entered in the dialog Cancel button Closes the dialog without updating the p
139. Low Quality Trim End button and an Analysis dialog box will appear Then click the Parameter button Select pSU2718 from the Vector Name list in the Trim Vector and Smal from the Cloning Site list F Trim ind F S END F Timaios f E Trin the frst 10 hp shie the quality e less than s F Fewo Ne PALI Promoter Vector ETE Sa a Mamm overlap breth corasiered a contannaton 2 be Minimum Matching Percentage considered as cortarunatan s Oat prera B the sequence eneth is lese than 100 bp output to M Others foide vector timenne eneth is bp output to D Others tolder CE o jw j Click the OK button Click the vector and low quality end trimming button Chapter 7 a of eee ie Ow DSR BP OA COT gt S865 watt eel ve ELELE ETIL Tutorial 299 Once a vector sequence is found in the input sequence Vector pSU2718 SmalI as the vector sequence part is displayed below the sequence and Trimmed Sequence is displayed in the Insert filed 7 4 5 Masking Vector Sequences sequence Select Vector pSU2718 SmalI in the result of the vector and low quality end trimming button to highlight the vector eee ee Oo pa pomo oe De T ERTE A418 trae rehen beet as OEEZ FILET COLS If under this condition you click the Mask button Wri on the toolbar the vector sequence is converted to N D po oe oF DSR sear ean eet ur ae emer er ve 2 o ESE S eGh as
140. MiraiBio DNASIS MAX User s Manual For Research Use Only Part no C 51125 10200 License Agreement i LICENSE AGREEMENT BEFORE OPENING THIS PACKAGE YOU SHOULD CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS BY OPENING THIS PACKAGE YOU AGREE TO BECOME BOUND BY THE TERMS AND CONDITIONS OF THIS AGREEMENT WHICH INCLUDES THE SOFTWARE LICENSE AND LIMITED WARRANTY IF YOU DO NOT AGREE WITH THESE TERMS AND CONDITIONS YOU SHOULD PROMPTLY RETURN THE PACKAGE UNOPENED TO MIRAIBIO INC Mirai or Mirai Distributor AND YOUR MONEY WILL BE REFUNDED The enclosed software is licensed not sold to you for use only upon the terms of this Agreement and Mirai reserves any rights not expressly granted to you You are responsible for the selection of the Software to achieve your intended results and for the installation use and results obtained from the Software You own the media on which the Software is originally or subsequently recorded or fixed but Mirai retains ownership of all copies of the Software itself LICENSE You may a Use the Software on a single machine at any given time b Obtain limited numbers of Copy Protection Devices Additional Copy Protection Devices are provided only as a convenience of running the software c In no manner engineer or reverse engineer the copy protection hardware or whole or part of the software d Copy the software only for backup provided that you reproduce all copyright and other proprieta
141. Moves the selected annotation or part one step down Moves the selected annotation or part to the top layer Bud Moves the selected annotation or part to the bottom layer Waveform Toolbar Icon Function Decreases the vertical width of tracing Increases the vertical width of tracing gt Decreases the vertical width of a view f Decreases the horizontal width of a view Increases the vertical width of a view Increases the horizontal width of a view Turns ON OFF the hand tool for scrolling through individual items of data in the parallel data mode Views hides a trace of lane A Views hides a trace of lane C Views hides a trace of lane G Views hides a trace of lane T Qi ay Selects a reference sequence for alignment only the FASTA format ACGT Hides an imported sequence i Switches back to the alignment display mode pe Makes an alignment between a trace indicated sequence and an imported sequence ATTE 7 Converts into a complement sequence Window Descriptions 1 4 Menu Bar ie Untitled DNASIS Efe Ek Sequence Yew Help File menu Function description New Opens a prompt dialog Open Opens a specified project file It is also possible to specify more than one file at the same time Save Project Stores a project by overwriting it Save Project As Stores a project by giving it a new n
142. NNNNNNNN NNNNNNNNNN NNNNNNNNNN NANA DE Sequence NNNNNNNNNN NNNNNNNNNN NNN NNN EDAG Seguence N NNNNNNNNNN NNNINNNNNNG CC GCCCC 90 100 Sequence i E BE CCETGTGAG GA Sequence SATGGGG CCCTGTGAG Sequence CRTGGERCEG M A CCCCTGTGAG Sequence CRTGRGGCER ACAGTEG AGE ACT CCCCTGTGAG GA 150 160 Sequence TGGCGT TAGTATGAGT GTCGTGCAGC CTCCAGG CC COCCO Sequence c GCGT TAGTATGAGT GTC CTCCAGG CC Sequence CTA GOGT TAGTATGAGT GTCGTG CTCCAGG CC C Sequence 200 Sequence GGAGAGCCAT AGTGGTCTGC Sequence AGTGGTCTGL Sequence GTGGTCTGC Sequence CCAT AGTGGTCTGC Chapter 3 Creating a Consensus Sequence Details of Analysis 119 This function uses the result of multiple alignment to create and display a consensus sequence based on the most conserved base at each position in the alignment In the drop down menu of the result window under Sequence select Make Consensus Sequence Sequence Sequence Sequence Consensus Sequence Sequence Sequence Sequence Consensus Sequence Sequence Sequence Sequence 10 20 30 40 50 TGECCECCEE TAAATGGGG CGACACTCCG CCATGAATCA CICCCCTGTG Ai GCCAGCECE CTGATGGGEG CGACACTCCA CCATAGATCA CTCCCCTGTE Al GECAGCCCE CTGATGGGGG CGACACTCCA CCATGAATCA CICCCCTGTG Ai GCCAGCCCC CTGATGGGEG CGACACTCCA CCATGAATCA CTCCCCTGTE AI TGCCAGCCCC CTGATGGGGG CGACACTCCA CCATGAATCA CTCCCCTGTG AI 70 80 90 10 110 GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTACA GI GTCTTCACGC AGAAAGCG
143. Quality 0 Sequence Quality Range Min 0 Min End Sequence Quality 0 Sequence Quality Range Max fi 00 Item Included Region Description Specifies a region where you want to design a primer Enter a region as follows startbp length Example Specifying 50 451 indicates a 451bp region starting from 50bp that is 50 500bp You cannot specify more than one region Start Codon Position Currently not supported Sequence Quality Enter a list of integers delimited with a space When specifying this parameter you must enter exactly one quality for each base Details of Parameters Min Sequence Quality Specifies the minimum value for the sequence quality within the sequence to be a primer Min End Sequence Quality Specifies the minimum value for the sequence quality within 5bp at the 3 end of the primer Sequence Quality Range Min Specifies the minimum value for the valid sequence quality Sequence Quality Range Max Specifies the maximum value for the valid sequence quality Penalty Weights for Primer x General Parameters Primer Picking Condtions Pre Sequence Inputs Penalty Weights for Primer Hyb Oligo Conditions Penalty Weights for Hy Oligo Penalty for Primers Tm Wtf Gt f1 Sze th Gf oczu fo Gtfo Set Complementanty 0 SN s 0 Mespiming 0 Sequence Quality 0 End Sequence Qualy 0 7 Seli Complementarity 10 Poston Penaky 0 End Stability
144. Repeat Search Searches and displays the results of tandem repeat position fora DNA or RNA sequence selected from the sequence editor Explanation of the Result Window et es lojx DPR a nE FBl A 2 2 i CEEL Ea F WyePrte Diya pp enten Eyre MND iep oTN Mor semer Map View Brn Ste Sawet x rig Ntt aoe ime P i T Fyrr Tepasi Sevrh a wm 20 w din sog Serch Sequxs JSooonstost aieiai tc steggoqgos oct gge tags colgnagegg 2 Repeete ep 2 Repeats 3 sp y f OOOO 3 Repeats tbe Eupan rs Sequence View Disp Se 2 Repent Tos Tiup mp 2 Rapeato t Gp 2 Bepeate te IAG bp 10 20 ae a ot agtgaGaatc atcg ats 1 Sbp 2 Repeats 5 6b 3 Repeats 2 dbp Tandem Repeat Area _ Map View Displays tandem repeat areas Click a tandem repeat area to color it as selected Sequence View Displays the sequences together with the tandem repeat areas Click a tandem repeat area to color it as selected Displaying a List of Search Results Refer to Displaying a List of Search Results in 3 16 Hairpin Loop Search Setting Parameters 1 Click the Tandem Repeat Search icon from analysis button view An Analysis dialog box will appear then click the Parameter button and the Tandem Parameterset Editor will appear 108 Details of Analysis Length _ a 10 t nod more than 2 repeats Default Cx Cancel
145. Results morina a E E E SA RRN AETS N AA A AE EAE 50 Browsing Annotations of Searched Common Motifs s sssssssssssssssssssstsrstsrsesrrssesrersisrersreterererererererere 151 Browsing Details of Searched Common Motifs cccccececeseeesceeeecscesesecseeeeseeecseescsesseeecsesseeeeseeesseeaee 51 3 35 Proteolytic Site Search cccccceeseeessceeesseeessneeseceeessaesesneeseseeeseesesneesssneeseneeesseseneeseenes 153 Explanation of the Result Wdowa aaa is aes EE EAE R E AA E 153 Selecting Proteolytic Enzymes to Be Searched for eesesesesessseseseseserrsestsesssssrsrsrsrsrersrnrerererrsrereree 53 Registering a New Proteolytic EnZyme cccecceccesesseeseeseeeeeeseeseeseesecseeeceaeeaeeaeeaeceeeeaeeseeaeeeseeeeaeeaeeneens 53 Displaying a List of Split Areas by Proteolytic Enzymes 154 Selecting a Proteolytic Enzyme to Be Displayed 54 3 36 BLAST Search AMINO ACid 0 ccccccecseesseeeeeeeeseseeescesesneeseseeeseaeaesaaesesneeseneeessaesenneesennens 155 Types 0f BEAST Search nts AN RE EE EEE jruses TE EOS 155 Explanation of the Result Wind OW s cccc cescestessasceseses cestacassessevaccavevelvcctsend ai e E E 155 Selecting a Database to Be Searched i sorier n n ER ERER EE RA 155 3 37 Internet BLAST Search Amino Acid ccceseseeeeeeeeeeeeeeeeeeeeeseeeeeenseeeeeeeaseeeeeeseeeeeeneeeeenens 156 Types Of BLAST Searches coiere E E E E R E TAR RR E 156 Explanation of the Result WINdOW scsnisiononyisriiieiiiiii
146. Sequence Color field for each base type 4 Click the OK button to close the dialog box Making Alignments with Reference Sequences Use of this function requires you to obtain a separate multiple alignment option You can calculate and display an alignment with respect to the reference sequence The feature of highlighting non matched sequences is extremely helpful in detecting SNPs 1 Read in the trace data as a candidate of the target to display 2 If more than one sequence is displayed click the one you want to set as the target 3 Click the S button on the Waveform toolbar and select a sequence file you want to use as the reference You can only specify a FASTA file here Click the Open button to close the dialog box 4 The reference sequence is displayed at the top of the sequence list 5 If you click the pe button on the Waveform toolbar the alignment is calculated and displayed The background of a non matched sequence becomes blue 6 To stop the alignment display click the ACGT button on the Waveform toolbar Scrolling through Multiple Waveforms Horizontally and Separately You can scroll horizontally through each of the waveforms displayed This function lets you align different waveforms at a specific bp position 1 Read in several waveform files to display at the same time 2 Click the a button on the Waveform toolbar when the mouse cursor changes its shape to am 3 Drag a waveform being processed 4 Cli
147. Shows the expectation of a matching part Any matching parts with a lower score value has higher similarity Selecting a Database to Be Searched other than one to one BLAST Search 1 Click the BLAST Search icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and BLAST Parameters will appear 112 Details of Analysis Program name blastn x Detail Expectation value fi 0 x Default IV Filter query sequence Descriptions 100 x IM Include gap in alignment Alignments 1100 ha m Nucleotide Database _JExample jIn House NA Select All MMAM 7 Deselect All Setting Help OK Cancel 2 The Nucleotide Database filed displays a list of databases Place a checkmark for the database to be searched 3 Click the OK button Obtaining an Entry to the Result of Search If the object entry for the result of search belongs to the GenBank database it is possible to obtain the entire GenBank Flat file of the entry Since this function links to the NCBI Web site via the Internet the Internet environment and the proxy server must be set Procedure Select an entry you want to obtain and click the Ep button on the toolbar You can select more than one entry by clicking the mouse while pressing the Shift key Chapter 3 Details of Analysis 113 3 20 Internet BLAST Search Refer to 7 1 3 Initial Setting This func
148. TAT PATS ARSOUAAGECTOARTAT T Description Specify the field for the entry search Search Key Input the search key for the entry search It is possible to enter alphanumerics and symbols Search button Click this button to perform a search If the search is successful a dialog will show the entry information that was found If not successful a message will appear Entry Shows the index number left and total number of entries right for the entry currently shown lt lt button If you click the button one entry before the current entry will appear However it is not possible to click if the entry currently shown is the first one gt gt button Click the button to show the entry after the current one However it is not possible to click if the entry 20 DNASIS Basics currently shown is the last one Import button Click the button to import the sequence of the entry currently shown into DNASIS ID Shows the ID of the current entry Database Source Shows the Database Source of the current entry Definition Shows the Definition of the current entry Updated Shows the update date of the current entry of BPs Shows the number of base pairs for the current entry Sequence Shows the sequence of the current entry Close button Click the button to close the dialog Obtain sequences from NCBI Entrez To start select the Retrieve sequences from NCB
149. TC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GI GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GI GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GI GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GI 130 140 150 160 170 CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GI CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GI CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GI CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GI The consensus sequence is added to the Sequence View 120 Details of Analysis 3 23 Phylogenic Tree DNA This function calculates a phylogenic tree by using all sequences that are currently displayed in the window The result of calculation is displayed in another window Explanation of the Result Window 0 MultipleAlignmentTr File Edi View Help P H Sequenceooao v BELLEKTE A029 Sequence0000 0 020 0 053 0 020 L 0 123 0 195 0 308 Sequencel011 Sequence 005 Sequencel 006 0 171 Sequencel001 0 166 Sequence0003 0 187 Sequencel028 0 180 0 049 Sequencel0 10 0 064 Sequencel0 12 0 068 0 085 0 014 0 036 0 170 Sequencel022 0 102 Sequencell24 0 200 Sequence 003 Sequencel0 13 0 145 0 163 L 078 Sequence0025 Sequence0018 Sequence0019 Sequencel023 Sequencel004 Sequence0007 p 115 Sequence0008 0 227 0 157 0 111 Sequencel020 Se
150. TGACCAGCTOGCAGA Cancel 4 File menu Description Export Stores all ORF data except for check boxes as tab delimited text with header in a file Print Setup Sets the paper size to use for printing Print Starts printing Close Closes the search result list Edit menu Description Copy Copies the selected ORF data except for check boxes to the clipboard as tab delimited text with header Select All Selects all the ORF data Check All Check all the ORF data in the list Uncheck All Uncheck all the ORF data ORF in the list Shape Setting Edits the status on Map View Details of Parameters View menu Description Show Only Checked Displays only the checked ORF data Show All Codons Displays all the ORF data including the Start Codon Stop Codon not in reading frames All Frames Displays all the frames Normal Frames Displays the frames of normal strands Complementary Frame Displays the frames of complementary strands Show Comment Displays comments in the Result List Show DNA Sequence Displays switching to DNA sequence Show Translated Sequence Displays switching to amino acid translation sequence Help menu Description Help Displays online help Toolbar S 4 aj 2lsle cle Description The same as selec ing Export from File in the menu The same as selec ing Print Setup from File in the menu
151. URNAL itself as the journal MEDLINE Imports a string excluding the string MEDLINE itself as medline FEATURES See Table 4 Regards the string FEATURES as the start of FEATURES Searches for FEATURES as a secondary search key If the Features Key is CDS imports the Product definition as the Feature name Start and End Otherwise imports the note definition as the Feature name Start and End If no definition is found imports the Features Key see Table 4 as the Feature name and import Start and End as blank ORIGIN Regards the string ORIGIN as the start of the vector sequence Import the lines up to the line as the vector sequence Features Key Table 4 CDS TATA signal CAAT signal promoter enhancer rep_origin polyA signal primer_bind misc_binding Defining Start and End You cannot import the definition of a join by setting the Start and End positions defined with the Features key You can import only the following definitions 1000 1100 complement 1000 1100 Features Key Features Key The following describes the sections that will be imported using an example with a GenBank file The search keys are shown in boldface type The sections to be imported are shown in italics with underlines LOCUS DEFINITION ACCESSION NID KEYWORDS SOURCE ORGANISM REFERENCE AUTHORS TITLE JOURNAL REFERENCE AUTHORS TITLE JOURNAL FEATURES Source gene HSU33203 309 bp mRNA PRI 20 SEP 1995 Human mdm2 E md
152. _ 3 Each item in the Features dialog box displays the current information 4 In the Features dialog box modify the Name Start and End and click the OK button Deleting a feature To delete a feature registered with the selected vector perform the following steps 1 Select the feature from the list and click the Delete button for the Features 2 When a message asking you to confirm deletion appears select Yes The selected feature is deleted from the database 3 Once the feature has been deleted the cursor moves to the first feature in the list Deleting a Vector To delete a vector perform the following steps 1 Select the vector you want to delete from the vector list in the vector management window 2 Click the Delete button 3 When a message asking you to confirm deletion appears select Yes The selected vector is deleted from the database Displaying References In the Vector Database Manager screen you can click the Reference button to view a list of reference information that is set for the vector AUTHORS Groskreutz D J and Schenborn E T TITLE Direct Submission JOURNAL Submitted 26 JAN 1996 D J Groskreutz R amp D Promega Corporation 544 Importing a Sequence from an External Definition File In the Vector Database Manager you can create a new vector by importing the contents of an external definition file To import a sequence perform the following steps 1 In the Vector Database Manag
153. ackground separately DNA sequences and amino acid sequences are also set separately 4 Click the OK button Displaying Pre Edit Original Sequences You can display pre edit original sequences those sequences available immediately after they are read from a file at the same time 1 Select View and then Preference Alternatively you can click the A button on the toolbar 2 From the dialog box that then appears select the Sequence tab 3 Place a checkmark in the Show original sequence check box 4 Click the OK button Sequences are displayed in a two row pattern the top row for original sequences and the bottom row for sequences being edited AF165046 Sequence tteggggoga cactccacca eed cectetgagg aactact tteggggcge cactccacca tagaccacth cectetgage aactact AF165046 Sequence aagcetctag ccatgecett agtatgagte tcgtgcagce tecaget aagegtctag ccatggcett agtatgagte tcgtgcagce tecaget AF165046 Sequence gagagecata etestctece gaaccegtga gtacaccega attgcca gagagecata gtggtctecg gaaccegtga gtacaccega attgcca AF165046 Sequence ctttcttgga teaacccgct caatgcctes agatttesec etgccce etttettgga tcaaccegct caatgccteg agatttegge etgccce AF165046 Sequence gccgagtagt ettegetcgc saaaggcctt etegtactec ctgatag eccgagtagt ettgggtcgc gaaaggcctt gtegtactec ctgatag a wore at wore wee renn Lmt a al a AF165046 Sequence gececgggag gtctogtaga ccgtgcatca tgagcacaaa tectaaa gececgggag etctcstaga cogtgcatca tgagcacaaa te
154. ains at least one of them If you do not specify any region DNASIS MAX will find the optimum primer from all regions of the input sequence Excluded Regions Specifies a region or regions you want to exclude from the primer sequence search Enter regions as follows startbp length startbp length startbp length Example 1 Specifying 50 2 indicates that the product will contain 2bp from a position 50bp away from the 5 end that is bases 50 5 bp Example 2 Specifying 50 2 80 5 indicates that the product will contain 2bp from a position 50bp away from the 5 end and 5bp from a position 80bp away from the 5 end that is bases 50 51 bp and 80 84bp 186 Details of Parameters Item Description To specify more than one region delimit regions with a space When more than one region is specified DNASIS MAX will design a primer and probe which do not overlap any of the regions Product Size Specifies the minimum value Min optimum value Opt and maximum value Max for the length of the PCR reaction product Number To Return Specifies the maximum number of primer candidates to be obtained Max Mispriming Currently not supported Max 3 Stability Specifies the maximum allowable value for Delta G necessary for duplex sequence dissociation at 5bp from the 3 end of the left primer and right primer A larger value makes the 3 end more stable Pair Max Mispriming Currently not s
155. ake here is common to Homology Search and Motif and Domain Search After setting once the first time you will not have set up again each time you log in If you use a proxy to connect to the internet you must set the proxy separately For details refer to 1 6 Internet Settings Dialog Box Procedure 1 Click the Option tab from analysis button view and click the GeneIndex Homology Search icon or GeneIndex Motif and Domain Search icon foe Untitled ONASIS Ble ed Sequence yew Help TETEE u aans lo vlE Se o s Gin a z w AF087301 231 bp DHA Tinesx onae Chlanydia trachomatis 344 transaldolase tal gene partial cds DNA Seach ACCESSION AF087301 aerer WErsT ow APO97301 1 GI 4140495 DNA Compare LEYUORDS a DNA Mulige Sequence SOURCE Chlanydia trachomatis z Aminoicid Basic L ES mroAcd Seach a m we m sm Aminodicid Compare aneno peen T 7 Aminodcid Multiple Sequence araw Aavetation ete teh i i Database Options SP DMASpace Automate 9 2 a E Contig Menager APOS 7201 Sequence aattcotggg acttgggsag gtatatgtge tgeagaggtt ttagaaagte Annotation soumre sowe 2 Gensindex Homology Search jE tal gre ji axed Uceuien 53 tal CDS s a mw w E N A E AFOR730 Sequence ttgteacgtg octttaattt ttaactctgt gonagcgate googcagons Annotation soume t source tal gee tal CDS 4 Exchange case of selected sequence Target AF057301 Postio
156. alignment profile is pre calculated data for the alignments between multiple input sequences that is saved for later use Why do want to use a profile Calculating multiple alignments requires a long time For example in the case of DNA DNASIS MAX requires only ten minutes to calculate multiple alignments for 40 data items but it may require two days for 200 data items This applies when the average BP length for the input sequences is about 1 5Kbp Longer sequences such as a gene or a complete genome require a longer time If you have many known sequences and want to calculate alignment between an unknown sequence and the known ones you can save the time required to calculate alignment with the unknown sequence by creating a profile first Calculating a profile requires the same time as an ordinary calculation However once a profile is created DNASIS MAX can calculate alignment with the unknown sequence much faster in about 10 seconds for the above example Disadvantages of using a profile Using a profile provides fast calculation However it results in degraded alignment precision The same data may produce different results when you use a profile and do not use a profile You should consider those characteristics when using a profile Procedure for Creating a Profile Like any other mode of analysis click the Analysis menu when creating a profile Here is a list of precautions 1 Read a sequence you want to create into the Main
157. ame Export Stores a sequence by giving it a name The file formats below are available FASTA format Text format Formatted text format MSF format DMP DNASIS Plasmid Map File format Import Sequence Obtains a sequence from a file The target is limited to those items of data that have undergone sequence conversion because of the need for checking the source file for integrity The target does not cover any file that is incapable of sequence conversion Print Setup Displays the Set Printing Information window and gives the setting of the paper size and printer information Print Preview Displays a print image Print Carries out printing Print Page Preview Displays a print image for the part that is currently displayed on the window Print Page Prints only the part that is currently displayed on the window Exit Terminates the DNASIS MAX Edit menu Function description Undo Cancels the previous operation Cut Cuts a sequence portion Copy Copies a sequence portion into the Clipboard Copy Image Copies the image of a displayed view into the Clipboard Paste Pastes any items of data on the Clipboard into a specified part Select All Highlights all the sequence data or comments where the cursor is located Select Range Highlights a range Sequence menu Function description NewDNA Adds a DNA sequence New Amin
158. an on screen preview of the printed image Page Setup Provides various print settings Exit Terminates View Edit menu Description Copy Copies the data in the window as a tabbed character string into the clipboard View menu Description Toolbar Toggles the toolbar to display or hide it Status bar Toggles the status bar to display or hide it 138 Details of Analysis Help menu Description About DNABasicAnalysisViewer Displays the version information for this View in the dialog box Contents Displays online help Button Description Ei Export button The same function as the Export menu Print button The same function as the Print menu Copy button The same function as the Copy menu Chapter 3 Details of Analysis 139 3 31 Isoelectric Points This function analyzes amino acid sequences and displays the result of analyzing isoelectric points Explanation of the Result Window Elle Edit View Help B frarsis70 z E Hg S a s electric Point Analysis Aninotcid Number pka lege ive gt e 2 His H n dherat ive ik 3 Asp 3 9 clu 4 43 4 Tyr 4 10 1 N_Terninal 5 C_Terninal Phelf 2 2 Isoelectric Point pI 4 5 6 Charge 7 20 00 10 00 8 0 00 10 00 i 20 001 29 4 5 6 8 S WO 1 12 13 14 ph Ready NUM 7 1 Amino acid name having positive charge 2 Amino acid name having negative charge 3 Charge weight 4 Num
159. an query length equal to or greater than the specified value The overlapping length for query length is the ratio of the number of matched bases to the query sequence length output header line If this check box is selected DNASIS MAX will add a header line to the output file output query sequence If this check box is selected DNASIS MAX will add a query sequence to the output file 218 Details of Parameters 4 28 Amino Acid Content No parameters Chapter 4 Details of Parameters 219 4 29 lsoeletric Point No parameters 220 Details of Parameters 4 30 Hydrophilicity Hydrophobicity and Secondary Structure et Editor Hydrophobicity Table hydrophobicity Hopp amp Woods Ej REFERENCE AUTHORS Hopp T P Woods K R TITLE Prediction of protein antigenic determinants from amino acid sequecces JOURNAL Proc Natl Acad Sci USA 78 3824 3828 1981 PMID 6167991 E2 Window Size p IV Amino acid usage I Isoelectric point we owes Item Description Hydrophobicity Always select this check box Hydrophobicity Table Specifies a table which defines hydrophilicity and hydrophobicity for each amino acid used for hydrophilicity and hydrophobicity analysis Window Size Specifies the window size when displaying hydrophilicity hydrophobicity and secondary structure Amino acid usage Do not select this check box Isoelectric point Do not s
160. anges the sequence name and adds the sequence Cancel Only the sequence with the same name is not imported Cancel All If multiple sequences are imported all of them are not allowed About Comments A comment is automatically given to a sequence that has been read from a file with any of the following formats FASTA GenBank Flat EMBL PIR and former DNASIS For the comment giving rules refer to the description for the file Chapter 2 DNASIS Basics 29 To display a comment click the button on the View Toolbar To hide the comment click the button again It is also possible to edit comments directly Refer to If several sequences are read and displayed the comment displayed corresponds to the target or activated sequence in About the sequence view pane The name of the current target sequence is displayed in the Sequence View and the Map View Target in 2 9 Editing and The current target sequence name is displayed on the Status Bar as well Analyzing Multiple Ba ONASIS Pro File Edit Sequence View Help Sequences S Be Sl l D a 6 oe 2 5 WE Sea was e ie OCUS DMPPY 1031 bp mRNA INY 12 SEP 1993 a EFINITION Drosophila melanogaster PP Y mRNA for protein phosphatase Y EC E Ee 2163 a al A e Proson phosptjetase Y m a E B ca mea n oO fay ie ee a 154801 Sequence tectesteee atcaaagcg gtgtcctgc ggcgggzagc ttesaacest zzwzagtg cats ion nares gt E yo7510
161. anzler Eck Kurf rstendamm 22 10719 Berlin Germany Tel 49 30 8877 2600 FAX 49 30 8877 2610 www hitachisoft bio com info bio hitachisoft de Japan Hitachi Software Engineering Co Ltd Life Science Research Center 1 1 43 Suehiro cho Tsurumi ku Yokohama 230 0045 Japan TEL 81 45 500 5111 FAX 81 45 500 5119 www hitachisoft jp dnasis hitachisoft jp Chapter 1 Window Descriptions 1 Chapter 1 Window Descriptions Window Descriptions 1 1 Main Window This section explains the Main window of DNASIS MAX izmera mn no PE pa Rese eee x Menu Bar ed Eaa LIC t TBP S4ece e3ate eli vy PuwSSh peewee Toolbar Comment View Map View View Toolbar ie NE WD 1 FO E Analysis Button View Sequence View Chapter 1 For details refer to Window Descriptions 3 1 2 Description of Individual components of Main Window Sequence View Pane The Sequence View Pane displays chromatograms sequence the results of sequence editing and the results of analysis maai Saee ICG 7 ine cer fom 1l teed Sega De Goals n 2 GT GiG mee Smm nee ALATA O46 ATTTM ECAJ a he s DE cer een e a vesa japam a s4 unea Tuwo Ga acTal cer eee eee 1 Indicates the sequence name 2 Indicates the analysis name Show saver tm Show Analysis Name Show Sequence Sn enn ae 3 Indicates the sequence 1 2 3 Map View Pane The Map View Pane provides a map style overview of the result of anal
162. ar 3 Porto a fhe ol arene the mating daw tren De you sash to contru Ce 3 Click Yes to display the dialog below Plasmid x Start point r Cancel Item Description Initial setting Start point Specifies the start position of the base sequence in the range from 0 to 359 0 unchanged 4 Specify the start position and click OK A plasmid map will appear in the editing area The plasmid map already on display will be overwritten by the one made from the imported file but the figures edited in Normal Mode will display Chapter 6 Create Plasmid Maps 277 6 5 Drawing in Normal Mode In Normal Mode normal figures such as lines arrows rectangles and spiral diagrams can be drawn and edited To create or edit figures in Normal Mode select Command gt Normal Figure or click 4s on the Toolbar While drawing in Normal Mode plasmid figures cannot be created or edited Add Normal Figures To draw normal figures click the icon for normal figures and drag from the starting point to the endpoint of a figure The following normal figures can be drawn Type Object Line Arrow Curve Rectangle Ellipse Polygon Text Text Label Text HOV Oe Add Spirals Two types of spiral can be drawn Spiral Type alpha Lr KYL 1 Click a on the Toolbar and drag the line that will be the center of the spiral while editing from the start position to
163. ar Select target databases for the GeneIndex Motif and Domain Search and click Next 5 For the sequence string the sequence shown in DNASIS MAX will display here in FASTA format And click Search The search results will appear 6 An Export to DNASIS button will appear in the Search Result window so click it and a DNASIS Export window will appear 7 Set the export parameter and click the Export to DNASIS button again to start the download If multiple sequences were displayed in DNASIS MAX they will also display in FASTA format under GeneIndex search conditions However Motif and Domain Search will only return a result for the lead sequence Upper Limit of Characters In Motif and Domain Search the maximum number of searchable characters after converting to FASTA format is 20 000 For details refer to Upper Limit of Characters in Homology Search of 3 44 Searches Using GeneIndex Export to DNASIS button If you log in to GeneIndex from DNASIS MAX the Export to DNASIS button will appear in the Homology Search Result Motif And Domain Search Result and Index Search Result windows If you click the Export to DNASIS button it is possible to export an associated compressed file to DNASIS MAX from a homology search result or motif and domain search result Exporting to DNASIS MAX The file downloaded when you click the Export to DNASIS button is compressed in LZH format Click Open from the dialog that normally appears when a do
164. arameter dialog box will appear 2 Select the codon table you want to change in the Codon Table in the Parameterset Editor window as shown in the figure To verify or edit the codon table click the button Open Reading Frame Codon Table fe hitial Godons Standard nd l 3 Click the OK button Chapter 3 Details of Analysis 85 Changing the Start Codon 1 Click the ORF icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear 2 Select the start codon you want to change in the Initial Codons field in the Parameterset Editor window as shown in the figure To verify or edit the start codon click the button Open Reading Frame Codon Table Universal 7 E hitial Godons 3 Click the OK button Listing the Result of a Search for ORFs For open reading frame result in sequence view select the sequence name and analysis name then click the Result List Dialog button All the ORFs are listed mixi File Edit View Help Bla gt 4 mhe Sle cfe l End Length MW Sequence 34479 26 ATGTACAACATGATGGA 3407080 ATGATGGAGACGGAGC 3393961 ATGGAGACGGAGCTGA 29837 39 ATGAACGCCTTCATGGT 2937386 ATGGTGTGGTCCCGCGG 28088 38 ATGGOCOAAGAGAATC 2728950 ATGOACAACTOGGAGA 2301680 ATGAAGGAGCACCCGG 20687 15 ATGAAGAAGGATAAGT 1875799 ATGGCGAGOGGGGTCG 1717527 ATGGACAGCTACGOGC 1647055 ATGAACGGCTGGAGCA 157005
165. arameters 198 Details of Parameters 4 17 Tandem Repeat Search Tandem Repeat Search Repest Length a 10 hp Repeat Gount more than 2 repeats Default ox Carcel Item Description Repeat Length Sets the repeat length If the repeat length is within the range specified here the repeat will become a hairpin loop region candidate Input range 2 to 99 Repeat Count Specifies the number of repeat regions If the number of repeat regions is above this number the repeat will become a tandem repeat region candidate Input range 2 to 2 147 483 646 Default button Returns parameters to default values OK button Closes the dialog after the parameters have been set with the values entered in the dialog Cancel button Closes the dialog without updating the parameters Chapter 4 Blast Parameters Program name IV Filter query sequence IV Include gap in alignment blastn X Expectation value fi 0 X Details of Parameters 199 4 18 BLAST Search DNA and Amino Acid Detail Default Descriptions fi oo X Alignments 100 bi m Nucleotide Database OK Cancel p Deselect All a Setting Item Description Program name PROGRAM Specifies the name of the program the BLAST search uses Select one of blastp blastn blastx tblastn and tblastx Use the following settings DNA BLAST search blastn DNA BLAST search protein DB blastx DNA
166. are Engineer ing HitachiSottware Eng ineer ing HitachiSoftware Engineer ingHitachiSoftwareEngineeringHit eoe e ea eee Ce LOC San es TIM EEEn eE Toh has too long name You can t export this enzyme DNASIS MAX does not export this data and proceeds to exporting next data No enzyme name If the selected proteolytic enzyme does not have a name the dialog box appears Manager dbtool Eq j r t You can t export no name enzyme f 5 DNASIS MAX does not export this data and proceeds to export the next data 262 Databases 5 11 BLAST Search Dedicated Database Use this window to create and manage sequence databases dedicated to BLAST search Refer to Select Sequence Database dialog box in 5 11 Blast Search Dedicated Database Window description TZA DNASpace Blast Database Manager E coliGenome ecolint TEST CA A A A UNA P P p P yeastnt Source DB Auto Update New 18 054 1998 3 16 6 21 Updated 1413 1986 7 2 6 21 Updated Delete 4067 1994 4 27 6 21 Updated 3266 1993 11 17 6 21 Updated Wate 808 1995 2 1 6 21 Updated ie 9 6 Updated Set Schedule 400 3 24 Updated 7 14 Updated Glear Schedule 3 24 Updated YH ecoliaa 4257 3 24 Updated IA yeastaa 6406 3 24 Updated DB Path M Scheduled Update 19997015 a000 H m Icon Description Ca This icon indicates that the database has been converted from a sequence database
167. art to cut the restriction enzyme is selected If there is more than one position to cut by the same restriction enzyme all of them are highlighted The part displayed in a red frame in the Map View is displayed in the Sequence View Selecting a Restriction Enzyme to be Searched for The restriction enzymes are registered in the restriction enzyme database The position to cut by the selected restriction enzyme is searched for from the database 1 Click the Restriction Enzyme Site Search icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button The RestrictionSiteParamEditor window appears Chapter 3 Details of Analysis 95 RestrictionSiteParamEditor Select from a Category Iv Recognition Length 5 IV 4base cutter IV Sbase cutter V Cut Kind IV 5 extended blunt cut JV 6base cutter IV Tbase cutter Select from a List User Selected 457 Ej r The number of cutting sites per enzyme MIN 0 V MAX 2 we mei 2 When searching for the length of recognition sequence or a cutoff select the Select from a Category item and check the target Recognition Length and Cut Kind If necessary designate the upper and lower limits for cut frequency When selecting a target restriction enzyme from the list select the Select from a List item and click Restriction enzymes registered in the Restriction Enzyme List will appear Als
168. ase stores in house DNA sequences such as the experimental data available mA This icon indicates that the database stores in house amino acid sequences Name Displays the name of the database of Seqs Displays the number of sequence data items stored in the database Date Displays the date on which the database was updated last Comment Displays a comment if any DB Path Allows you to set the path of the directory to store the database 232 Databases 5 4 Vector Database You can list information about the vectors registered in the database Window Description a Ector Name m Cloning Site p Features Name Position CPosition Stat End Features Xbal 1934 38 49 244 promoter hol 32 36 280 1932 firefly luciferase BamHI 2196 2200 303 281 GLprimer2 sequencing primer binding Hindlll 245 249 1964 2185 SY40 late poly A signal Hpal 2094 2094 2272 2253 R primer4 sequencing primer binding Balll 36 40 2510 2510 ColE1 derived plasmid replication orig Kori 5 1 aa 3977 htacactamase ml ctor Data Vector Name ESF pGL3 Promoter Vector er 5010 Cloning vector pGL3 Promoter firefly lucifera U47298 Edit Add Delete Edit Add Delete Sequence ggtaccgagc tcttacecet gtcagcaacc cacccattct ctcagectct caaaaaactt aagaaaggcc aaggctatga atagtcccge ccectaactce gcccateccg ccectaactc cgcccagttc cegccccatc actgactaat tttttttatt
169. ata refer to 7 1 Before Starting the Tutorial D o we oe Oe ose O fr 2 O8 448 238 t 2 ti vor s3an PESER YLONA f Oni Bom iamini PEE EEEEEET 7 3 3 Specifying the Database as the Target of BLAST Search It is necessary to set the search conditions before performing a BLAST search Select the DNA Compare group on the analysis button bar Blast Search Protein DB Click the BLAST Search button and an Analysis dialog box will appear Then click the Parameter button and the parameter setting dialog box for BLAST search will appear showing the list of the various DNA sequence databases currently installed on the PC in the Nucleotide Database This tutorial will use the mammalian database MAM so make sure only MAM is selected and click the OK button Chapter 7 Tutorial 293 BCT Example _ InHouse NA IMAM Deselect All UniGene_Hs_Uinig 7 3 4 Running BLAST Search Click the BLAST Search button and Analysis dialog box will appear Clicking the Execute button starts BLAST search on the MAM database At the end of analysis the result window appears Data 1 Homoley Search Results Viewer 40 50 MN 50 20 80 200 9 200 ateacescatt i e Ii cacccaca Alces alces witochondrial ote 420 ell Tragelaphus spekii nitechandr 2397 Se 77 Cervus nippon talousnus mitoc 233 7e 076 Tragelaphus eurycerot cylochr 230 1e 074 Rangifer tarandus mitoc
170. ater size Gt than the optimum product size Product Tm Specifies penalties for a lower Tm value Lt and a higher Tm value Gt than the optimum Tm value Celsius for the product Tm Difference Specifies a penalty for different Tm values between primers Any Complementarity Specifies a penalty for a higher complementarity than the optimum between primers Hyb Oligo Penalty Weight Specifies a weight used to calculate penalties for a primer pair and a probe 3 Complementarity Specifies a penalty for a higher 3 end complementarity than the optimum between primers Pair Mispriming Currently not supported Primer Penalty Weight Specifies a weight used to calculate penalties for a primer pair Hyb Oligo Conditions Details of Parameters 189 PrimerParameterEditor xj Genesa Parameters Primer Picking Condions PreSewenceirouts Penaky Weights for Primer Hyb Oigo Conditions Penshy Weights for Hyb Olgo Hy Oigo Excluded Regon Hyb Oligo Sze Ma fie Ofo Ma 27 Hyb Oligo Tm Mn 57 Opt fo Mo fc Hyb Oligo GCF Ma fo of o Max 0 Hyb Oligo Sel Complementary 12 Hyb Oligo Max F Self Complementary n2 Max N s fo Hyb Oligo Max Poh X Bo Hyb Oligo Min Sequence Quslty 0 Hyb Olgo Max Mishyts 12 Hyd Oligo Salt Concentration 50 Hyb Oligo DNA Concentration 50 Item Hyb Oligo Excluded Region Description Specifies a region or regions you want to exclude from the probe design
171. aving Tm closest to the optimum value Max Tm Difference Specifies the maximum allowable value for the difference between Tm for the left primer and that for the right primer Product Tm Specifies the minimum value Min optimum value Opt and maximum value Max for the Tm value Celsius for an amplification sequence Product with the designed primer DNASIS MAX will not select a product having Tm lower than the minimum value or higher than the maximum value When you specify the optimum value DNASIS MAX will select the product having Tm closest to the optimum value if the Product Size for Penalty for Primer Pairs is other than 0 The product Tm value is calculated using the following formula Tm 81 5 16 6 log10 Nat 0 41 x GC 600 length Na sodium conc GC GC content length sequence length Primer GC Specifies the minimum value Min optimum value Opt and maximum value Max for the primer GC content Max Self Complementarity Specifies the maximum allowable value for an alignment score when local alignment is applied to a Chapter 4 Item Details of Parameters 187 Description single primer or between the left and right primers You can use this value to predict the trend in self annealing for PCR A score is calculated with the following values EComplement base 1 00 N 0 25 Mismatch 1 00 Gap 2 00 gaps larger than 2bp are now allowed Max 3 Self Comple
172. base Data Source Set a DNA sequence or amino acid sequence and initial data Blank Nucleotide Create an empty DNA sequence database Blank Amino Acid Create an empty amino acid sequence database FASTA file Nucleotides Read DNA sequence data in the FASTA format FASTA file Amino Acid Read amino acid sequence data in the FASTA format Comment Enter a comment You can leave this field blank Chapter 5 Databases 231 Summary of the Parameter Set and Description of Each Parameter Sequence DB Updater Pararneterset Editor Source Data in house tasta Select target databaces f l Empoy database betore updating Update related bias database atte updating E Mahe new biss database d dose awst P Exarole Item parameter Source Data 0 Name aseg Date Comment TAPIR 239764 2001 8 3 The database is derived from the IA In Houe tu s 2001 1071 2001 11 16 Description GenBank FASTA Not supported by the current version of DNASIS In house FASTA Usually select this item Select target databases Select the database you want to update You can select one or more databases P This icon indicates that the database stores public DNA sequences mainly GenBank Each entry in this database has the same unique ID as that used in the original database we This icon indicates that the database stores public amino acid sequences A This icon indicates that the datab
173. base where the subject sequence has been registered Sequence Type Shows the original database where the subject sequence has been registered Example gb GenBank emb EMBL dbj DDBJ etc Identifier Shows the identifier of the subject sequence Definition Shows the definition of the subject sequence Length Shows the length of the subject sequence Score Shows the score of a match A match with a higher score value is higher in similarity E value Shows the expected value ofa match A match with a lower score value is higher in similarity Identities Shows the percentage of the matching bases or amino acids within the entire length of a match Positives Shows the number of groups in which the score has a positive value within the entire length of a match when the query sequence and the subject sequence are compared for each amino acid Overlap Length Shows the length of a match Gaps Shows the total number of gaps inserted into the query sequence and the subject sequence This cell remains blank when there is no gap Strand Shows the direction of the match for example from 3 to 5 or from 5 to 3 Matching Percentage Shows the matching rate Query Start Shows the start point of a match in a query sequence Query End Shows the end point of a match in a query sequence Target Start Shows the start point of a match in a subject sequence Target End Shows the end point of a match in a subject sequence Query Length Shows the length
174. ber of amino acid residues 5 Residue at N end 6 Residue at C end 7 Isometric point 8 Charge and pH graph File menu Description Export Exports the data in the window into a text file Print Prints the window Print Preview Displays a printing image Page Setup Provides various print settings Exit Closes the window Edit menu Description Copy Copies the data in the window as a tabbed character string into the clipboard View menu Description Toolbar Toggles the toolbar to display hide it Status bar Toggles the status bar to display hide it 140 Details of Analysis Help menu Description About DNABasicAnalysisViewer Displays the version information for View in the dialog box Contents Displays online help Button Description Export button Exports the data in the window into a text file It is possible to export data for each part Print button Prints the window Copy button Copies the data in the window as a tabbed character string into the clipboard a Horizontal View Expands the view horizontally Expansion button f Horizontal View Shrinks the view horizontally Shrinkage button Vertical View Expansion Expands the view vertically button Vertical View Shrinkage Shrinks the view vertically button S H E Help button Displays online help Chapter 3 Details of Analysis 141 3 32 Hydrophilicity Hydrophobicity and Secondary Structure This function analyzes the hydr
175. bete tr ae oaran Vean Ten pa S pho qes t iy ophotany am a Alpha Heks M_L m As a result you can display as many analysis results as you like side by side Interlocking the Range of Selection among Results of Analysis You can interlock the selected ranges of multiple analysis results With several analysis results for the same sequence displayed providing the analysis results or the sequence with range selection causes the selected range to be interlocked automatically Such an automatic interlock occurs even when there are several selected ranges This makes it relatively easy to compare the locations of functional parts of the sequences Creating Analysis Buttons Having Different Parameter Setting Changing parameters each time analysis is performed can be tedious Frequent changing of parameters could be needed in such situations as when selecting a database for homology search selecting an enzyme type for restriction site search 44 DNASIS Basics and providing a codon table for translation You can solve this problem if you duplicate analysis buttons and associate each with set of desired parameter settings Right click an analysis button you want to duplicate 1 From the menu select Duplicate DNA Basic Base Usage cou Tol oy Codon Usage By Large Icon DNA Search DNA Compare X Delete DNA Multiple Se Duplicate Amina
176. binations to perform a translation 2 If the combination does not match any entry in the Codon Table that combination is translated into X 3 If more than one codon matches the function checks whether all the amino acids translated as non X are identical If all are identical they are translated into the same amino acid If one of them is different that is translated into X The method for replacing characters is as follows R gt GA M gt A C B gt GT C V gt GC A Y gt T C S gt GC D gt GA T N gt A C GT K gt GT W gt A T H gt A C T Example 1 Translating AAH Because AAH is not found in the Codon Table it is treated in the following way Of AAH A is not a replaceable character so that it is not replaced H can be replaced with A Cor T Accordingly AAH can be replaced with any of the following AAH AAA AAC and AAT AAH AAA AAC AAT Using the replaced character string the function searches the Codon Table again to perform atranslation The first AAH does not exist The next AAA can be translated into the amino acid of K No 43 in the table Similarly AAC is translated into N No 42 in the table while AAT is translated into N No 41 in the table Because all the three results K N N are not the same amino acid AAH is translated into X Example 2 Translating TCN Because TCN is not found in the Codon Table the character string becomes the target of translation Of TCN T and C are not replaceable charac
177. box displays the current information 4 In the Cloning Site dialog box modify the Name Position and CPosition and click the OK button Note If you click the OK button without setting the CPosition the Position setting is automatically copied to the CPosition Deleting a cloning site To delete a cloning site registered with the selected vector perform the following steps 1 Select the cloning site from the list and click the Delete button for the Cloning Site 2 When a message asking you to confirm deletion appears select Yes The selected cloning site is deleted from the database 3 Once the cloning site has been deleted the cursor moves to the first site in the list Modifying a Feature You can add modify or delete a feature Adding a feature To add a new feature to the selected vector perform the following steps Chapter 5 Databases 235 1 Click the Add button for the Features 2 The Features dialog box appears Features x Features sep sut O wf oe omen 3 In the Features dialog box set the Name Start and End and click the OK button 4 Once a feature has been added the cursor moves to the added feature Modifying a feature To modify a feature registered with the selected vector perform the following steps 1 Select the feature from the list and click the Edit button for the Features 2 The Features dialog box appears Features Nene SIE Stat 280 Eng 1932 Cox __concet
178. box will appear Then click the Parameter button The dialog below appears 150 Details of Analysis Analysis Parameter xj Select Parameter Nucleic acid Motit eme 2 Select Collect Motif Results then click Set The dialog below appears Collect Moti Kesutts Porameterset bitor Check collect motd condtarn Connon mele n aa thal E gacet F Common mat s i more than sepen Erehe notits tourd more than timer n orne sequence F Exchade motits toud more than tines n total T Pek w top 5 notite we _ oan o j Item Common motifs in more than X sequences Description Select to designate as common motifs when they are common in more than the specified percent sequences for motif search results input simultaneously Common motifs in more than X sequence Select to designate as common motifs when they are common in more than specified number of sequences for motif search results input simultaneously Exclude motifs found more than X times in one sequence Select to exclude motifs found more than the specified number of times in a certain sequence Exclude motifs found more than X times in total Select to exclude motifs found more than the specified number of times in all the sequences Pick up top X motifs Select to designate specified number of common motifs counting from the largest number of motifs found Motifs with the same number are all regarded as commo
179. c tree C J een e Description Corresponds to the tree parameter of Clustal W Bootstrap tree Select this check box when evaluating the reliability of the tree using the bootstrap method Corresponds to the bootstrap n parameter of Clustal W 206 Details of Parameters Number of bootstrap Corresponds to the bootstrap n parameter of Clustal W Seed no Corresponds to the seed parameter of Clustal W Exclude positions with gaps Corresponds to the tossgaps parameter of Clustal W Correct for multiple substitutions Corresponds to the kimura parameter of Clustal W Chapter 4 Details of Parameters 207 4 22 Phylogenic Tree DNA and Amino Acid The parameters are the same as 4 21 Multiple Alignment describes 208 Details of Parameters 4 23 Creating Multiple Alignment Profiles DNA and Amino Acid General General PairwiseAlinment NultioleAlienment ProteinGap Tree Profile Nane gt P Profile Manager Sequence Type DNA Output Order Order by Alianed Use FAST Aleorithm for the slignment Protein Chars ABCOEFGHIKLMNPORS AOZ DNA Chars ABC OGHKMNAS TUVWY Default Item Profile Name ret me Description Specifies a profile for storing the results of multiple alignment calculation To create a new profile click the Profile Manager button to open the Multiple Alignment Profile Manager If there is another profile stored under t
180. caaaaagctt ggcattcceg tactettgst aaagccacca tegaagacgc caaaaacata aagaaagecc cggceccatt ctatccacts gaagatggaa ccectggaga gcaactgcat aagectatga agagatacec cctesttcct ggaacaattg cttttacaga tgcacatatc gagstggaca tcacttacgc tgagtacttc gaaatgtccg ttcgstteec agaagctatg v Edit New Delete Import Export Reference Help 298 Tutorial To register vector sequences for vector trimming click the Import button and specify the pSU2718 prm vector sequence file which is located under the VectorData folder of the database installation destination For a standard installation you need to specify C HSK_DB VectorData pSU2718 prm a ou ree Met se ene Pal osme wame ere meg 1m na DVE ee p ar rm Im Flared are sg pee toto so mi 4 eea teen me mee my acceagc tcttacecet ectagcoces ectceagatc teceatctec atctcastta 2 stcagoaacc stastoocsc coctasctoc socostoocs wactc cacocast tc cacceattct ccaccecate acteactast tttitttat tatecassss Cteggoctct gagctattcc agaagtasts agsagecttt tttesagece t ttte H Cansansctt anticae eeeecceccs ageeeecec Conasecets Ceaceccat a emastagaa ccact eenan aasectaten apagatace cctesttcct geaacaatte cttttacaga a seactenece toacttecec tenstecttc anastetoca ttcasttasc asmasctste j pe ee ee G a 7 4 4 Carrying Out Vector Trimming Select the DNA Basic group on the analysis button bar Select the cloning vector that was used for sequencing and its cloning site Click the Vector and
181. caatece p 250 250 cittcltees tcascccect caateccted Line amp bp aa bp aa Line 10 20 err er ees ce Wr ev er 1 aaaaaataat aataacaatc Line Displays only the scale line above the sequence n a ad r l ttgatcctga ttccagtttg Show positions at the sequence head Assigns the bp indication to both the right and left ends of each line of a sequence For alignments the value is smaller by the gap 4 Click the OK button Changing the Font for Sequences You can change the font for sequences 1 Select View and then Preference Alternatively you can click the A button on the toolbar Chapter 2 DNASIS Basics 39 2 From the dialog box select the Font tab 3 Select Sequence in the combo box at the top 4 Using the Setting button set the font 5 Click the OK button Select a font with equal width otherwise the display may crash Note that the color setting here is ignored Changing the Color of Sequences You can change the color of sequences 1 Select View and then Preference Alternatively you can click the A button on the toolbar 2 From the dialog box select the Sequence tab 3 Perform the setting within the Sequence Color box F When checked this item displays sequences in the color mode When unchecked it provides a black Colorize sequence view disol isplay Oeit Sets the color on a character basis You can set the color of characters and the color of the er item b
182. can create an empty profile delete a profile modify the attributes of a profile import and export a profile Multiple alignment profile What is a profile A multiple alignment profile is pre calculated data for the alignments between multiple input sequences that is saved for later use Why do want to use a profile Calculating multiple alignments requires a long time DNASIS requires only ten minutes to calculate multiple alignments for 40 data items but it may require two days for 200 data items This applies when the average BP length for the input sequences is about 1 5Kbp Longer sequences such as a gene or a complete genome require a longer time If you have many known sequences and want to calculate alignment between an unknown sequence and the known ones you can save the time required to calculate alignment with the unknown sequence by creating a profile first Calculating a profile requires the same time as an ordinary calculation However once a profile is created DNASIS can calculate alignment with the unknown sequence much faster in about 10 seconds for the above example Disadvantages of using a profile Using a profile provides fast calculation However it results in degraded alignment precision The same data may produce different results when you use a profile and do not use a profile You should consider those characteristics when using a profile Window Description Rew Pw ya Profile list Disp
183. ccording to a specified number of characters 1 Click the button on the toolbar 2 Alternatively select View and then Preference In response to a dialog box that then appears set Fold Sequence on the Folding Ruler page to Fold by every xx bp aa Eguena treet eee aani amp e pe amp Dg erator a Ntttt Fe SSS Dshwat 79 gt amp amp xt 7 Z anis mean 7 fr Lal a ime a x m F ere 5 ial mea ven o tare neem Oo Oma Come unag s If block based display mode is chosen in conjunction with the options to fold back characters according to a specified width the value for the block length must divide the value of specified width without a remainder Inserting Spaces after a Specified Number of Characters Block Based Display Mode The block based display mode makes it possible to insert a space into characters each time a specified number of characters is reached 1 Select View and then Preference Alternatively you can click the z button on the toolbar 2 In the dialog box that then appears select the Folding Ruler tab fiz oeene menn eee anaj i pome ie ae ove se atBt gt 28 S38 22 gt gt 8S DeGwiat 7 Oma pee aei 3 Place a checkmark in the Block Length check box 4 Enter a value into the Block Length item to serve as the block length For the method of folding back characters according to a specified wi
184. ccordingly Fold by every bp aa Displays a sequence by folding it back according to a specific number of characters Block Length bp aa Displays a sequence by inserting a space after a number of characters Show Scale Checking this parameter causes the ruler to be displayed Line amp bp aa Displays both the scale line and the bp indication above a sequence In the case of alignments displays the bp count for the consensus sequence bp aa Displays only the bp indication above a sequence In the case of alignments displays the bp count for the consensus sequence Line Displays only the scale line above a sequence Show position at the sequence head Assigns the bp indication to both the right and left ends of each line of a sequence For alignments the value is smaller by the gap Initialize Initializes all settings to factory presets Use Defaults Stores the settings Chapter 1 Window Descriptions 1 6 Internet Setting Dialog Box HTTP Proxy Tab internet Parameters a xj HTTP Piow FTP Firewall Mat Sewer prompdnasiscom ts Port feoeo User Name B Password as No Prony I Use Peasy Serve 13 Item Description Server Specifies the address of a proxy server to connect to the Internet Port Specifies the port number of a proxy server to connect to the Internet User Name Specifies the user name if the proxy server requires user authentication Password Specifies the pa
185. cel022 0 102 Sequencel024 Sequence 003 Sequence 013 0 068 0 065 0 014 i 0 036 0 180 0 145 0 200 0 183 1 0 079 Sequencel025 0 131 Sequencel018 bee a 0 143 Sequence0019 TL _ _ 119 Sequence0023 Sequencel004 Sequencel007 0 018 0 053 4 0 164 0 128 0 013 quence 002 p 9 115 0 111 0 041 0 063 4 Sequencel008 0 072 0 227 Sequence0020 0 157 0 205 0 167 0 179 0 147 0 030 0 127 Sequencel017 0 053 Sequencel 027 Sequencel021 Sequencel014 Sequence0015 Sequence0016 Sequencel029 Sequence 026 Sequence Count 30 Zoom 100 7 Refer to 3 23 Phylogenic Tree DNA for details 126 Details of Analysis 3 25 Creating Multiple Alignment Profiles This function creates a profile for a multiple alignment The multiple alignment between input sequences is calculated in advance and saved as a profile This allows high speed alignment calculation between an unknown sequence and the profile The Clustal W method developed by J Thompson and T Gibson is used as an engine for alignment calculation What is a profile A multiple alignment profile is pre calculated data for the alignments between multiple input sequences that is saved for later use Why do want to use a profile Calculating multiple alignments is computationally intensive and can require a long
186. ch as rectangles and helices 266 Create Plasmid Maps 6 2 Create a Plasmid Map 1 Select a sequence in Sequence View 2 Select Option from the Analysis Category in Analysis Button View and click Plasmid View Options S DNASpace Automation EA Contig Manager Plasmid Map 3 The plasmid map of the selected sequence will appear Command Edit Regulation Object Normal Object Plasmid Help Bel Hea oael ee Mil 4 Plasmid Figure Chapter 6 Create Plasmid Maps 267 6 3 Map Editing Window aioi xi Gemi OM bapian Cimina Chem teal i Menu Bs Sleleicls Sol ois iAl slala opt eli ssica z Toolbar Editing pane sj f fant ES Status bar 6 3 1 Menu Command Menu Export Template Description Exports the current status to a template Import Template Reads in and displays figures from a template Preview Displays a print preview Print Starts printing Normal Figure For inputting and editing normal figures Normal mode Plasmid Figure For inputting and editing plasmid figures Plasmid mode Exit Closes the Figure Editing window Edit menu Description Cut Cuts the selected object Copy Copies the selected object Paste Pastes the cut or copied object Undo Cancels the previous operation Redo Restores the canceled operation Properties Displays the properties of
187. ch bes thant 0 F Cokrize Sequence Amine Acid Combo box for selecting amino acid 5 Double click Background or Foreground then set the color on the color palette 6 Repeat Steps 4 and 5 as required 7 Click the OK button Editing and Analyzing the Result of Translation 1 In the result of translation drag the cursor to select the portion of the frame you want to edit or analyze as shown in the figure x96997 Sequence L orn OS Loeb a i ee x96997 Sequence ecegecetga accagcgcat ggacagctac gcgcacatga acggctggag ER AlaGlyV alA snGlnArgMe tAspSerTyr AlaHisMetA snGlyTrpSe adreAlaees ThrSerAlaT rpThrAlaTh rAreThr Thr laGlyd reGlyAreG uProAlaHis GlyGlnLeuA reAlaHisG udrgLeuGlu 790 200 810 820 83 X96997 Sequence tacagcates tecageaota goteesotoc cozcarcaco ceeecotcad EER TyrSerMetM etGindspG nLeuGlyTyr ProGInHisP roGlyLeuds aThrAlawee CysAreTHPS BPTrpAlaTh FArESerThr AreAlaserT euGInHisAs pAlaGlyPro AlaGlyLeuP roAlaAlaPr oGlyProGin 850 860 870 880 804 X96997 Sequence sccectcasa tecascccat ecaccectac zacstgagcg ccctgcagta GER AlaAlaGIni etGinProMe tHisAreTyr Asp alSerA lalLeuGInTy aProleudre CysSerProC YeTHrAl TA rThr tt la ProCysSerT reAreSerAs pAlaAlaHis AlaProLeuA reAreGluAr ProAlaVal 90 920 930 940 95 X96997 Sequence accagctcec agacctacat gaacggcteg cccacctaca gcatgtecta 2 Click the button on the toolbar 3 The Amino Acid window appears This window
188. ck the OK button Creating and Editing a New Table 1 Click the Hydrophilic Hydrophobic Search button from analysis button view and an Analysis dialog box will appear Then click the Parameter button 2 Click the button in the Hydrophobicity Table field Window appears 3 Click the New button to display the New Hydrophobicity Table as shown in the figure New Hydrophobicity Table Enter the name of new hydrophobicity table omei 4 Enter the name of a table you want to create and click the New button The display returns to the Hydrophobicity Table Editor window 5 In the Hydrophobicity Table Editor window edit the contents of the table you created 6 Click the OK button to return to Amino Acid Basic Analysis Parameterset Editor 7 Click the OK button Chapter 3 Details of Analysis 143 3 33 Motif Search Amino Acid This function searches for the motif of data about amino acid sequences There are two available methods one uses a database and the other searches for any pattern you have entered Explanation of the Result Window Motif Ch Cat jommo Yew ib Ose RASA 1B 4s 24a ce 2a x as ONA Bese DNA Seach ONA Compare Anm Bee Map View Motd Seed Sequence View iodin ph Sequence Mote ewch Se ae a ee ee arnis fer nnnasfwlip pellililse evesevelew Lvype snoLveosytaTion z RENI 10 150 160 170 cis silceinfit
189. ck the am button on the Waveform toolbar again to return to the normal mode 60 DNASIS Basics Copying Trace Data You can copy trace data into the Clipboard after converting it to numeric values or graphics This function is very helpful for report making because it lets you copy only a specified range in the form of graphics This function also allows high resolution printing of the copied graphics Use the following procedures to copy numeric data 1 Drag a waveform to select a range as shown in the figure KELJ SET 57T 58T GG AGGTGTGGGAGGTTTTTNAANGCAAGTAAACCTCTANAAAT GG AGGTGTGGGAGGTTITTIINAANGCAAGT AAA TCT NA AATSG 630 640 650 660 NNTCCTTATTAACCCTTTANAA TTAAAAGCTA NNT TATTA CT NAA TTAAAA G CTA 380 690 TTATTAAAGCNN NCCONTA TIATTAAAGCNN NC 2 Right click to display the pop up menu 3 Select Copy Trace Value 4 Paste the copy into another application such as MS Excel as shown in the figure E Microrott excel Book ioii E fle Edt yew Insert Format Tools Qeta Window Help alaj xi DUSA n Ar H BD PF 3 Al D E E Em 0 0 6 113 0 0 8 113 1 0 10 100 2 o 8 79 3 3 7 54 4 10 4 32 4 2 1 15 3 x 1 4 2 61 4 2 1 s 9 7 l 0 102 14 13 0 116 19 19 0 121 21 24 0 7 18 2 0 105 14 24 0 86 8 19 0 61 3 13 0 3 a 8 1 21 2 4 4 9 12 1 9 1 Ei 0 7 0 54 0 p 2 65 0j E 5 119 o id 4 gt PiN Sheet1 Sheet sees GT Ole Ready Sum 123896 NUM Use the following procedu
190. comments for the proteolytic enzyme if any Check All button Selects the check boxes of all the displayed enzymes Uncheck All button Clears the check boxes of all the displayed enzymes Check Selected button Selects the check boxes of all the selected proteolytic enzymes Uncheck Selected button Clears the check boxes of all the selected proteolytic enzymes Show All button Displays all proteolytic enzymes in the database Show Selected button Displays all the selected the proteolytic enzymes Show Checked button Displays all checked the proteolytic enzymes Show Unchecked button Displays all unchecked the proteolytic enzymes Help button Displays online help OK button Sets the checked proteolytic enzymes to the enzymes that the method will use and exits from the Parameter Set Editor Cancel button Exits from the Parameter Set Editor without saving changes to the parameters Proteolytic Enzyme Database Manager button Starts the Proteolytic Enzyme Database Manager 222 Details of Parameters 4 32 Annotation Annotation Setting dialog Setting Dialog Annotation Name DP2 Annotation Kind fons Link URL fhttr awancbinlmnihgov entrez viewer fcgi val 604479 Show Link Annotation Range Ho 2320 input annotation range 1 2320 r Orient Ga c none m Part Range J Start End Add 141 1301 Jete Edit Comment 7 Key Value
191. ctaaal Displaying Complement Sequences You can display the complement sequences of sequences being edited at the same time 1 Select View and then Preference _ Alternatively you can click the A button on the toolbar 2 From the dialog box select the Sequence tab 3 Place a checkmark in the Show complementary sequence check box 4 Click the OK button 5 Sequences are displayed in a two row pattern the top row for sequences being edited and the bottom row for complement sequences The content of the bottom row is automatically updated while it is synchronized with the process of editing the content of the top row 40 DNASIS Basics AF165046 AFI65046 AF165046 AF165046 Sequence Sequence Sequence Sequence Sequence Sequence a PP PP PP tteggggcge cactccacca ober aacceccece etgagetest atcteeteal ccctgtgagg gegacactcce aactac ttgatg eee eee oe eee eer E eran eres Soares eraser ee ccatggcett agtatgagte tegtgcagce aagegtctag ttegcagate hirsiset ggtaccgcaa teatactcac agcacetcge siias tecagg aggtec gagagccata etctcggtat stestctecs caccagacec gaaccegtga ettggccact gtacaccgga catetggect attece taacgg ctttettega gaaagaacct teaaceeget agttegecea caatgcctgg gttacggace agattteggc tetaaacceg etgece cacegs gecgagtagt eggctcatca ettegetcec caacccagcs gaaagecctt etttecggaa gtggtactsc caccatgacg ctgata
192. current window 3 End Trim at least Trim the first Same as 5 End If this check box is selected DNASIS trims the 3 end If you select both Trim at least and Trim the first DNASIS MAX will first trim as specified with Trim at least and then trim as specified with Trim the first Unconditionally trims the sequence of the specified length from the 3 end Selecting the check box enables trimming Specify an integer of 0 or greater as the sequence length If this check box is selected DNASIS MAX trims the low quality portion from the 3 end Specify an integer of 0 or greater for the window length and quality threshold for determining quality Trimming is performed as follows 1 Calculate the quality of the sequence window of the specified length from the 3 end 2 If the quality is lower than the threshold in step 1 shift the window one base toward the 5 end and repeat step 1 3 When the quality becomes equal to or greater than the threshold in step 1 trim the portion starting from the 3 end and ending at the N that is closest to the 3 end within the current window Specifies whether the conditions for trimming the 5 end are also applied to the 3 end Selecting the check box causes DNASIS MAX to use the same conditions for the 5 and 3 ends 182 Details of Parameters Item Trim Vector Description Specifies whether to trim a vector sequence To trim a vector select the check b
193. d Note The primers whose Tm values are smaller than this value cannot be designed Opt The primers whose Tm values are as close to this value as possible are designed Max The maximum Tm value for the primer to be designed Note The primers whose Tm values are larger than this value cannot be designed 4 Click the OK button Changing the Length for a Primer to be Designed 1 Click the Primer Design icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear 2 Select the Primer Picking Conditions tab in the Parameterset Editor window as shown in the figure Penalty Weights for Primer Hyb Oligo Conditions Penalty Weights for Hyb Oligo General Parameters Primer Picking Conditions Pre Sequence Inputs Primer Size Min fis Opt fo Max a7 Primer Tm Min fr Opt feo Max jes Max Tm Difference 100 z E Product Tm Min Opt Max Primer GC Min poo Dpt Max foo Mar Self Complementarity 8 Max 3 Self Complementarity 3 Max N s p Max Polyx Boo Inside Target Penalty PE Outside Target Penalty pooo First Base Index e CG Clamp fo Salt Concentration 50 Annealing Oligo Concentration 50 M Liberal Base Default Cancel 3 Set the following values in the Primer Size field Min The minimum length for the primer to be designed Note The primers whose length is shorter than this value cannot be designed
194. d DNASIS MAX will extract all items that have both the value specified with Primary Keyword and that specified with Secondary Keyword even if the specified number of extracted items is exceeded Pick up items that Extracts all items that satisfy the specified conditions from the results of homology search You can specify conditions for each of the matching percentage number of bases matched score and expectation value All the conditions specified here are ANDed If two or more conditions are specified DNASIS MAX will extract the items that satisfy all those conditions matching percentage is more than If this check box is selected DNASIS MAX will extract targets having a matching percentage equal to or greater than specified value Chapter 4 Details of Parameters 217 Item Description overlapping sequences are more than If this check box is selected DNASIS MAX will extract targets having a number of base matched equal to or greater than the specified value score is more than If this check box is selected DNASIS MAX will extract targets having a score equal to or greater than the specified value E_value is less than If this check box is selected DNASIS MAX will extract targets having an expectation value equal to or greater than the specified value overlapping length for query length isIf this check box is selected DNASIS MAX will extract targets having an overlapping length for more th
195. d recognizes are displayed separated by Bases Indicates the base number of the recognized sequence Kind Of Cut Indicates the shape of the cut performed by the restriction enzyme 5 extended Cuts the sequence so that the 5 end is longer than the 3 end 5 GAATTC 3 3 CTTAAG S 3 extended Cuts the sequence so that the 3 end is longer than the 5 end a 3 ACGCGT S blunt cut Cuts the sequence so that the 3 and 5 ends have the same length not identified 5 CCCGGG 3 3 ACGCGT S Indicates that the position to cut cannot be identified for the restriction enzyme Even when this enzyme is checked it will not be registered as a parameter Button Description Show All Displays all the restriction enzymes in the database Show Selected Displays all the selected restriction enzymes Show Checked Displays all the checked restriction enzymes Show Unchecked Displays all the unchecked restriction enzymes Check All Check all restriction enzymes Uncheck All Uncheck all restriction enzymes OK Sets the checked restriction enzymes to the enzymes that the method will use and exits from the Parameter Set Editor Cancel Exits from the Parameter Set Editor without saving changes to the parameters Restriction Enzyme Database Manager Starts the Restriction Enzyme Database Manager Chapter 4 Details of Parameters 193 Restriction Site Param Editor dialog RestrictionSite ParamEditor
196. der When the program starts up a prompt dialog box will appear xj p eom A amp Ar sequence gt Sequences from tiks WH Ani fet ec Retr irine sequences from databern g Retr kvine sequences Yom NCBI Enter Ae flee Open existing project in EXKSK_DG Tutor is Dota Calroddindnsrs D ENHSK DEETitor islata NutioleAkennent dasi 2 EWHSK_DGeTutorialDatas Tyrosine ieee Phong yletionS he dnasis e C o 7 2 2 Using the Editor to Open Sequence Files Select Create a new project from the prompt dialog For Type select DNA and for Content select Sequences from files then click the OK button Specify Tutoriall fsa from the dialog box that appears Open Files BEI Look in fa TutorialD ata e Ce Eg a Calmodulin fa a Cytochrome_C fa a Hemolysin fa i MultipleAlignment a Myoglobin fa a Porin fa E DEREI Filename O Files of ype Al Fies C7 era y LA 7 2 3 Running ORF Search Select the DNA Search group on the analysis button bar Primer Design Bl Oligo Probe Design Chapter 7 Tutorial 287 Click the ORF button E and an Analysis dialog box will appear Analysis x B o Comment Searches the open reading frames I Execute analysis without showing this dialog Click the Execute button to start an ORF search with 3 frames When the analysis is finished the results will appear in map view and below the sequence in the
197. diting Sequences AUdVANCEA cceseeeeeeseeneeeeeeeneeeneeceeeeneeeeeeenseseeeseseeneeseseeeeesesesneeeeessnenens 41 Selecting Sequence Ranges 41 Converting Uppercase and Lowercase Characters 41 Masking Sequences s ssssssseseeseseseeesereeeeeen 41 Converting into Complement Sequences Reverse Complement Sequences and Reverse Sequences 41 Returning to the Pre Edit Original Sequences ees eseeeeeeeseesseeecseescsecseerseeseseeseescsesaeeesseeeeseeaee 42 2 8 Analyzing Sequences advanced cccccesenteeeeeeeeeeeeeeeeeeeeeeneeeaseeeeeeeseeeeeenseeeeeeeeeeeeennssnenens 43 Displaying Results of Analysis Side by Side oo cee ese cseeeeseeseeecseescsececsecseeeeseeseeesseeecsesaeeesseeeeeeeaee 43 Interlocking the Range of Selection among Results of Analysis 0 ccceecceeseeeseeseseeseeeceeeeeeeseseeseeeees 43 Creating Analysis Buttons Having Different Parameter Setting eee eee eeeeeeeeeeecseeeeseeeeeeeeee 43 Changing Analysis Names in display ccceecesesceseseeseeseseeeeseeseseeacsecseeacsecaesaeseeacsesseaesesaseeeseeeseneaees 44 Renaming Analysis Buttons sss s cicssiscissuessectcussassitztes aeanesesseazezecacsnacassaisaderssunsvessedzabact iauseaysuisibarsansesassenseess 44 Deleting Analysis Buttons sissecssssscessvesssuecceayevn cs croanescessevscauseaceseeaneuscesavanestoaacesdevevatesuedacercevsuatesaeiseerdasese 45 Changing the Order of Analysis Display necne aE E KEEK RR 45 Repositioning
198. dth Fold by every xx bp aa you can specify only a value by which the line width can be divided without a remainder 5 Press the OK button Hiding the Ruler You can hide the ruler from the Sequence View 38 DNASIS Basics inizi De GR Somer pe io ou eae Ite b JE 4 2 24 838 227 ee 238 Dehw an o gt fe JOJO lO i E 1 Select View and then Preference Alternatively you can click the A button on the toolbar 2 From the dialog box select the Folding Ruler tab 3 Uncheck the Show Scale item 4 Click the OK button Ways of Displaying the Ruler There are several ways of displaying the ruler Examples are the methods of using the scale line and bp indication 1 Select View and then Preference Alternatively you can click the 3 button on the toolbar 2 From the dialog box select the Folding Ruler tab 3 Perform the ruler setting Line amp ol Displays both the scale line and the bp indication above the sequence For the alignment based ine aa p display it shows the bp count for consensus sequences bp Displays only the bp indication above the sequence For the alignment based display it shows aa p the bp count for consensus sequences 7 80 tigsssscea coctccacce tagotcact ecatgecett agtatescte tizteca sagcstetag ccatgscgit agiatsag 130 140 aagestciog ccatgscgit agtatgagig sogasccota stestctecs saaccss 190 20 gagegccata gtegtctece gaaccestea ethictteca tcaacecect
199. e Clicking this button opens a file dialog box that lets you select the motif database to import DNASIS MAX does not import a motif database if it already contains a database having the same name Export button Exports the selected motif database This button is disabled if no database is selected or if more than one database is selected Clicking this button opens a file dialog box that lets you specify where you want to export the motif database to DB Path button Allows you to specify the location of nucleic acid motif databases If the list does not display any registered databases you can click this button to specify where you want your databases stored The Nucleic Acid Motif Database Directory dialog box appears Help button Displays online help Editing the Properties of a Motif Database 1 In the analysis button view click the DNA motif database 2 The Nucleic Acid Motif Database Property dialog box appears as shown in the figure You can use this dialog box to view and edit the properties of a DNA motif database The following describes details about the dialog box 254 Databases Item of Motifs 812 Comment This database contains 312 nucleic acid motifs a Database Name Database Name SAMPLE Last Modified Date 2001 9 21 Cancel _ I DB Lock oid Description Name of the motif database The database name must not exceed 64 characters It cannot contai
200. e Nhel elctagc Sacl eaectlc sat eltceac smal ccclees al tletaga i etal 1526 0 1 0 blunt cut 1 3 extended 0 5 extended 0 5 extended 1 987 5 extended 0 3 extended 0 5 extended 0 blunt cut 2 5 extended 0 DABRARBABABABAAD 2 After the search completes the restriction enzymes that cut the sequence are listed Place a checkmark for the restriction enzyme you want to display and click the OK button Selecting a Sequence that Contains a Cut Piece If you click the region between two sites in the Map View area the fragment is displayed in the predefined color and the sequence of that fragment is also selected alt te GA Sama fe tee bea Bee SGhitBl 2 aawes eamertee s FRESE Be Bulae i fe cs Amral Ave Sen eaten ssn a Se voam Uadd Seamer AGMAT TOTTTITOT CTTCRSATTY TroTaasema TICON eke Dera Peeves ort fred a j p COLE EOI Looking for a Restriction Enzyme That Cuts Out a Specified Range 1 In the sequence select the range you want to cut out with the shortest overhanging length 2 In the Sequence View right click and select Search Optimum Enzyme from the menu The Search Optimum Enzyme Options window appears Chapter 3 The number of using restriction enzyme C Only 1 enzyme er C 1 or 2 enzymes oeei Details of Analysis 97 Only 1 enzyme Searches for an optimum restriction enzyme that cuts out the sel
201. e Report Displays a dialog box used to set parameters for extraction BLAST Search Refer to 4 18 BLAST Search Make Report Collect Homology Results Parameter Editor 3 items Primary Keyword Secondary Keyword MatchingPercentage E Over lapping E I Pick up all items with the same value C Pick up items that Jo Score ie more than J matchine percentage ie mote thar gt overlapping sequences ate more thar po and P Evalue ie less than pr and Jo overlapping eneth for query leneth ie mote than 95 E and fi 00 and JV Output header line I Output query sequence Help Item Pick up top items Primary Keyword matching percentage Cancel Description Sorts the target list in descending order by Primary Keyword and Secondary Keyword ascending order for E Value and extracts a specified number of entries from the top Specifies a primary key used to sort the target list Match ratio between the query sequence and target sequence at a homology matched portion Overlapping Number of bases matched between the query sequence and target sequence Score Score for a homology search E_value Expectation value for a homology search Secondary Keyword Specifies a secondary key used to sort the target list You can specify the same items as those for Primary Keyword Pick up all items with the same value If this check box is selecte
202. e and analysis name are underlined Renaming Sequences You can change the sequence name which is found at the leftmost column of the Sequence View or Map View using the following procedures 1 In the Sequence View click a sequence name you want to change The name then becomes the target and is now underlined 2 Click the name again 3 After a 0 5 second delay the outer frame is displayed in which you can perform editing as shown in the figure 32 DNASIS Basics Refer to Restrictions for Naming Sequence in 2 9 Editing and Analyzing Multiple Sequences Sequence AF244977 Sequence ttet 4 After editing press Enter or click somewhere outside the frame Sequence names involve usable character and length limitations Restrictions for Naming Sequences Sequence names have limitations on the length and characters that can be used Characters that can not be used lt gt Length Up to 128 characters Chapter 2 DNASIS Basics 33 2 5 Analyzing Sequences basic Analyzing Sequences 1 From the Analysis Button view on the Main Window find the analysis you want to perform 2 Click the Analysis button as shown in the figure oe Untitled DNASIS File Edit Sequence View Help jo eG s heeg o S fir int fr aa DNA Basic E r DNA Search a oe r 3 If you perform an analysis in which parameters can be set or edited by you an Analysis dialog wi
203. e and then Lower Case or clicking the E button on the toolbar Conversion from uppercase to lowercase characters Selecting Sequence and then Exchange Case or clicking the button on the toolbar Conversion from lowercase to uppercase characters and vice versa What is to be converted is different depending on the working condition whether or not there is a selected portion Yes Converts only the selected portion of the sequence If there are several selected portions all of them are converted No Converts the entire of the sequence Masking Sequences You can mask selected portions of sequences The masked portions are replaced with N for DNA sequences and with X for amino acid sequences Masking makes it possible to skip the selected portions to be analyzed 1 Select Sequence and then Mask or click the BD button or the SD button for amino acid If there are several selected ranges all of them are masked Converting into Complement Sequences Reverse Complement Sequences and Reverse Sequences Sequences being edited are converted into the following complement sequences reverse complement sequences and reverse sequences Selecting Sequence and then Complement or clicking the MP button on the toolbar Conversion into complement sequences 42 DNASIS Basics quce Selecting Sequence and then Reverse or clicking the button on the toolbar Conversion into reverse sequences TEG Selecting Seq
204. e clicked it is possible to change the type and thickness of the drawn line 2 Input necessary information and click OK The restriction enzyme will be changed Also when the Restriction enzyme position is changed the figures will be moved to the corresponding positions Change the DNA It is possible to move or change the size of the DNA name text area by using the mouse Figures can also be changed by changing the DNA properties The operation is described below 1 Select a DNA and click on the Toolbar The Plasmid Component dialog will open 274 Create Plasmid Maps OMS ie Fa ed Dr star pent Dhat Dee henge fra kx Item DNA Name Description Specify the DNA name using up to 50 single byte characters DNA start position Displays the start position of the DNA This item cannot be changed DNA end position Displays the end position of the DNA This item cannot be changed DNA base length Specifies the number of bases of the DNA Minimum value 1 Maximum value Plasmid base length number Direction Selects the direction of the DNA Clockwise forward Counterclockwise backward Non direction When tabs other than the DNA Tab are clicked it is possible to change the arrow line type and color 2 Input necessary information and click OK The DNA will be changed Also when the DNA base length is changed the end position will automatically be changed Additionally wh
205. e conaidered aa contamination a N Output options If the sequence length is less than 109 bp output to I Others toller I vector trimming length 0 bp output to Others folder M Output trimmed sequence ax N Vector DB Menseer Defoult Cencel Help Item Trim End Description Specifies whether to trim the end To trim the end select the desired check box 5 End Trim at least Trim the first If this check box is selected DNASIS trims the 5 end If you select both Trim at least and Trim the first DNASIS will first trim as specified with Trim at least and then trim as specified with Trim the first Unconditionally trims the sequence of the specified length from the 5 end Selecting the check box enables trimming Specify an integer of 0 or greater as the sequence length If this check box is selected DNASIS trims the low quality portion from the 5 end Specify an integer of 0 or greater for the window length and quality threshold for determining quality Trimming is performed as follows 1 Calculate the quality of the sequence window of the specified length from the 5 end 2 If the quality is lower than the threshold in step 1 shift the window one base toward the 3 end and repeat step 1 3 When the quality becomes equal to or greater than the threshold in step 1 trim the portion starting from the 5 end and ending at the N that is closest to the 3 end within the
206. e data Protein Weight Matrix Corresponds to the matrix parameter of Clustal W You can select BLOSUM series PAM series Gonnet series or Identity matrix which sets the value blosum pam gonnet or id respectively Alternatively you can select User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating similarity among amino acid molecules DNA Weight Matrix Corresponds to the dnamatrix parameter of Clustal W You can select IUB or CLUSTALW 1 6 which sets the value iub or clustalw respectively Alternatively you can select User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating scores which specify whether DNA matches or does not match Use negative matrix Corresponds to the negative parameter of Clustal W Selecting the check box enables the parameter Note Initially a positive matrix is used If this parameter is selected a negative matrix is used Chapter 4 Protein Gap Details of Parameters 205 MultipleAlignmentParameteriditor Cia xj GeneralSettings PairmizeAlienmert MultipleAlignment ProteinGep Tree Redia Soecitic cant ff I Eyecrophilc ept off Hydrophilic Residues Gap Separation Distance 100 I End Gap Separation IGPSNDOEKR 0 Item Residue Specific gap off Corcel Help Description Cor
207. e for Amino Acid Sequences 0 ccceceseceseeeeecscescsececeecseeesseesesesseeecseeeseeseeeaees Entering and Editing Multiple Sequences 0 ec ceeeecceeseeeeeeeseeeteeseneteeneeaes Switching between DNA Sequences and Amino Acid Sequences for Display 2 3 USING EXISting FilGS isso ete saceeeiasndecccetsneevsdacerecaxsucenpeaiecestecatacetegacnee tasectareesnaeceedsiarev ek acaveceviete 24 Opening Sequences fromthe Men spes soies Tan A add E eid EERE A O Opening with the Drag and Drop Method ccceceeccesseseeseeseesseeeeesceaeeseeseceeesecaceseeaeesececeeeeseeaeeaeeeeeentes Reddable File Formats 1 2 iaases sss sS ese ais da cyte SAE sacs aE seavetvasectbtgeses Reading Files tn the FASTA Format 0 005 csecescdesscese cesses a dacsnesdes steed dapteassvapiend aves NNN eee Reading Files in the GenBank Flat Format oes Reading Filesin the EMBE Formate cccesseweescosezedsassveccceesevecetsunauccacsavedstsnnanisertqieensbane ERER aed Reading Files inthe PIR POrni at xc3 se scvecccevesvaisisssc sescea vases Ra A a A E OT EOE E Reading Files in the Old Version DNASIS Format s s ssesssessesessssrsesststsrsrstsrsrerersrsrsrererererereresereneses 26 Reading Files im Text Formatet ser i a E E REEE REEERE ORERE ER 26 Reading Trace Data Files in the ABI SCF and ALF Formats eseseseseseseresseessssrersrsrsrsrsrsrsrsrsrsrerrsnes 26 Reading Multiple Fl ss rasne enna E ana E NRE R ORR 26 About the Sequence Name Abou
208. e of Setup you prefer then click Mest A Popleal Pregram vill be installed with the mort common opt lore Recommended for mort users Compact Program wil be installed with minimm required opt ions Cyrtom Tow say choose the options you went fo install Recommercked fer edvanced users cent Setup Type Window This Tutorial uses the file in the TutorialData folder in the Sample Database Installation Destination folder For initial setting it refers to the file contained in C HSK_DB TutorialData 7 1 2 Data Used in the Tutorial This section handles three versions of Tutorial which are stored in the files listed below 7 2 Open Reading Frame ORF Search Tutorial1 fsa 7 3 Blast Search Tutorial2 fsa 7 4 Vector Trimming Tutorial3_1 abi Tutorial3_2 fsa 7 1 3 Initial Settings Some parts of this Tutorial require a connection to the Internet Depending on your network environment you may need to configure the internet settings for DNASIS Max From the View menu in the Sequence Editor select the Internet Options item to display the settings window alternatively you can click the Internet Options button on the toolbar Our example here attempts to set the proxy server in the HTTP protocol for Web browsing Chapter 7 Tutorial 285 HTTP Proxy FTP Firewall Mail I Use Proxy Server If you are not familiar with proxies ask your network manager or refer to Internet Explorer for the s
209. e than one line Displaying Reverse Complement Sequences You can display the reverse complement sequence of trace data 1 Click the oe button on the Waveform toolbar The waveform displayed is in reverse time order resulting in a reverse complement sequence Switching to the DNA display mode under this condition will retain the status of the reverse complement sequence If there are several waveforms that have been displayed click a target waveform that you want to display a complement sequence Editing Sequences While Viewing Their Waveforms You can delete or replace bases while viewing their waveforms To delete bases select a range you want to delete and press the Del key To replace a single base select the base you want to replace and key in the new base Selecting 2bp or more will cause the replacement of the base to fail Use the following procedures to insert bases 1 Viewing the waveform makes a range selection of 2bp of the base before and after the point into which you want to insert a base 2 Click the button on the View Toolbar to switch to the DNA display mode 3 To use the Insertion Pointer click somewhere in the highlighted 2bp range which was selected in step 1 4 Enter a base from the keyboard 5 Select the range of the base entered in step 4 The range selection helps you recognize the region when you switch to the waveform display mode 6 Click the button on the View Toolbar to switch to th
210. e waveform display mode Returning to the Original Condition when Editing You can cancel the entire process of editing a sequence and return to the original sequence 1 Click the button on the View Toolbar to switch to the DNA display mode Chapter 2 DNASIS Basics 59 2 If there is more than one sequence click the sequences to set them as the target 3 Select Sequence and then Revert 4 When a confirmation dialog box appears click the OK button 5 Click the button on the View Toolbar to switch to the waveform display mode Hiding Specific Lanes You can display or hide the A C G and T waveforms If you click the A 5 G T or button on the Waveform toolbar the corresponding waveform is hidden and the base sequence italicized The toggle button allows you to switch between the display and hide modes each time it is clicked Expanding and Shrinking Displayed Waveforms You can change the vertical and horizontal scales of the waveform display area Reduces the display area vertically Expands the display area vertically Reduces the display area horizontally fe Expands the display area horizontally Changing the Color of Waveforms You can change the colors of waveforms and bases 1 Select View and then Preferences and click the gl button on the toolbar 2 This displays the Preferences dialog box in which you should click the Sequence tab 3 Enter a value for the
211. e you create does not have a palindrome structured recognition sequence Enter the recognition sequence using a complex code containing characters from the string ACGTURY WSKMBDHVN not case sensitive Enter an exclamation mark at the position to cut Specify the characters in the direction from 5 to 3 Text area for the number of bases Automatically filled with the same length value of the Normal recognition sequence excluding an exclamation mark If you enter a recognition sequence in the Complementary area it must have the same length excluding the exclamation mark as that specified here Combo box for the Kind of Cut Automatically selects the cut shape for the restriction enzyme OK button You can click the OK button to register the new restriction enzyme created This button is disabled if DNASIS detects any of the following errors in the data you have entered 1 The Enzyme Name text area does not contain a restriction enzyme name 2 The Normal text area does not contain a recognition sequence 3 The Normal text area contains a character other than ACGTURYWSKMBDHVN and 4 The Normal text area does not contain an exclamation mark or it contains more than one exclamation mark 5 The Complementary text area contains a recognition sequence including a character other than ACGTURY WSKMBDHVN and 6 The Complementary text area contains a recognition sequence without an exclamation mark or more
212. ected range using one type of restriction enzyme 2 enzymes Searches for an optimum restriction enzyme that cuts out the selected range using two types of restriction enzyme 1 or 2 enzymes Searches for an optimum restriction enzyme to cut out the shortest length using one type of restriction enzyme Alternatively uses two types of restriction enzyme in case that is more effective 3 Specify any of the choices and click the Search button to search for a restriction enzyme 4 The found position to cut is displayed in the predefined color Display Restriction Enzyme Fragment List Displays a list of fragments obtained by cutting the target sequence at the point of restriction enzyme sites To display the restriction enzyme fragment list select the sequence name and analysis name then click the Result List Dialog button in Map View or Sequence View or click in the Restriction Enzyme Fragment List dialog Enzyme Anal Results O xj File Edit View Help ERI mla No Start End Length Sequence aaaaaataataataacaatcatceeceeceectegatcegccaga eeeceecaacagcateeceagceceetceceetegececceecc eeecctcaacececaceececcectcagatecagcccatecacci categectcestecteaactcceageccagctccagcccccctete gatctegageaaagaaaactacecaaaactttttaaaaettctacte aacagcaacaaataaateectegateattaatteaataagtactctc 98 Details of Analysis 3 14 Motif Search This function searches a DNA sequence for one or more motif s There are t
213. ed The following describes the procedure for modifying different types of information Modifying the definition accession vector name or vector type 1 Select the vector from the vector list and click the Edit button 2 The Vector dialog box appears 3 Each item in the Vector dialog box displays the current information 4 Modify information as required and click the OK button If you do not want to modify information click Cancel 234 Databases Vector x Vector None EEA Type of Vector Linzer Det inition rumen mdm2 E mde2 mRNA compete cds Procession on Loa Modifying a Cloning Site You can add modify or delete a cloning site Adding a cloning site To add a new cloning site to the selected vector perform the following steps 1 Click the Add button for the Cloning Site 2 The Cloning Site dialog box appears 3 In the Cloning Site dialog box set the Name Position and CPosition and click the OK button Note If you click the OK button without setting the CPosition the Position setting is automatically copied to the CPosition 4 Once a cloning site has been added the cursor moves to the added site Modifying a cloning site To modify a cloning site registered with the selected vector perform the following steps 1 Select the cloning site from the list and click the Edit button for the Cloning Site 2 The Cloning Site dialog box appears 3 Each item in the Cloning Site dialog
214. ees 162 Procedure for Creating a Profile tornien ees ia o a Ea A E SONO ERREN RECON 162 Using a Created Profile on Anothet POsyesiieesnie naea a REAR 162 3 42 Using Phylogenic Tree Profiles Amino Acid snnnssnnssunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnne 163 Amal ysis POC UE r ss E E E 163 Explanation of the Result Window si s00 i ce asatadidan teh vaietanbinieasicaeschiasubin abies OREO 163 3 43 NCBI Entrez Search ccccccceecee cece essceeesnneeeeneeseceaessaesesneeseseeessaeaesaesesneeseseaessesesneeseenens 164 Explanation of the Search Window s piaia cay saledis raaire EEE AEE ATS IE sondage 164 Explanation of the Result Window sensence nei e Ea ae E EEE E E E EE as 165 3 44 Searches Using Genelndex Obtaining Accounts eee Bs Set Genelndex Server Informations eiss5 icsesseseisizesscanaces caine suaevees EAE AA EEEE Homology S arch eines ie elie leds edd eae besa E A ENTREN Motif atid Domains Searels sss esa coves secs vida A A A da cae en E EEEE AORA E Export to DNAS IS Dutton seein EE OE EE EEE E E E ERRE D EON Exporting to DNASISMAX ss r ei IEEE EE EE E Eie E AAEE RSA E EATE AAEE Parameter Set List and Parameter Meamings ssssssssssssesesecerssenensssevscnsseeseesesensonsssesesnssseae ss 172 About Genelndex 232 c2 53 et ies i eee LB LL 172 Contents Chapter 4 Details of Parameters cccceceeeeeeeeeeeeeeeeeeeeeeeeeeeenaeeeeeeeeeeeeeeeeaaanens 173 A 1 Com
215. elect this check box Chapter 4 Details of Parameters 221 4 31 Proteolytic Site Search Proteolytic Site Parameter Editor Proteolytic Enzyme List Z Wome Receeniton Seq Comment I ere an Acrosin KRIX Acrosin GathepsinB1 RIX CathepsinB1 CathepsinG LYFIX CathepsinG Chymosin FIM Chymosin Chymotrypsina Fy wx Chymotrypsina Show All MW ChymotrypsinG FYLIX ChymotrypsinG Show Selected Clostripain RIX Clostripain Show Checked Cocoonase KRIEX Cocoonase CyanogenBromide MIX CyanogenBromide Show Unchecked Elastase AX Elastase Help Enteropeptidase DDDDK I Enteropeptidase i se ARRET me ees zi Proteolytic Enzyme Database Manager Item Check All Cancel Usable Characters Setting Description Name of the proteolytic enzyme DNASIS MAX will perform analysis using the enzymes for Proteolytic Enzyme Name NAME which you select the check boxes on the left Recognition Sequence SITE Sequence recognized by the proteolytic enzyme An amino acid sequence is represented in the single character format with an exclamation mark indicating a cut position If there are two or more recognition sequences a slash is used as a delimiter If there are two or more recognition amino acids complex code they are enclosed by X indicates any amino acid Example KR X AR X Identify KX RX and ARX and cut between K and X R and X and AR and X Comment Displays
216. ement understand it and agree to be bound by its terms and conditions You further agree that it is the complete and exclusive statement of the agreement between us which supercedes any proposal or prior agreement oral or written and any other communications between us in relation to the subject matter of this Agreement iv Contents Contents LICENSE AGREEMENT 2222c280ncccs cancer cae a aaae iaraa riaal GOVERNMENT LICENSEE RESTRICTED RIGHTS LEGEND 2 02 eeceeceeeeee I PrETACC et ec E eS A SRS A A AS ee Ae EXILE Chapter 1 Window Descriptions cceceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeseeeeee T 1 4 Main WindOW iioii ausat aii visite ih ni viii Gn nts 2 1 2 Description of Individual components of Main Window ccccesseeseeeceeeeeseeeeeeneeeeeees 3 Sequence View Pane ses csy cseedsssschs szcsceueshedsuuasecassnysesseas sesYeu es seg E s ospusesdes s2bssusdeasasaeestva seeds 3 Map View Pantie essee nee eenn En EEEE E EA EEE ENEE E EAN E RESE a 3 Comment View Pane feces sc eers oooi aeon EN E Goss TEE EN Sous cue EEES NO se Cade PESE NEVE EE EEE ESSE 3 Analysis Button V OV P AO a E 4 1 3 Toolbars ainsi nwa Aine atid no RAN ein Anne ens 5 Switch Pane Toolbar cece aro EOE E sta tete eee eae Cue ROM e ars E T 5 Other TOO bars a rier neraso NESS eNe EEVEE E EEEE EES SE EEA EK VEENEV NE 5 1 4 Menu Bat ia e eis aa aaa a a svete seeds ey ca sda sedis sv eve a a aE aa eed Sa
217. en non direction is specified or the length is shorter than the arrowhead the arrowhead does not appear Change Annotation Length Drag the handle at the annotation start or end position to change the length Change the Length Drag the handle at the annotation start or end position to change its length Move the Position along the Circumference Drag the handle in the center of the annotation to move along the circumference Move the Position Perpendicular to Circumference Drag the handle next to the center of the annotation to move in a direction perpendicular to the circumference The size changes automatically when moving this way Chapter 6 Create Plasmid Maps 275 Figures can also be changed by changing the annotation properties The operation is described below 1 Select an annotation and click on the Toolbar Or change the annotation length and move along the circumference by using the mouse The Plasmid Component dialog will appear Armin line fre x toraman ferret hon thee penton Araton end porter Denote Item Description Annotation Specifies the annotation using up to 50 single byte characters Annotation start position Specifies the start position of the annotation Minimum value 1 Maximum value Plasmid base length number Annotation end position Specifies the end position of the annotation Minimum value 1 Maximum value Plasmid base length number Direction
218. enacenevaataseadasassiwestieiesadaaandvente svenswanatenstedinadinssieventsteducdanstvense 98 Explanation of the Result Window ccccccscssssesseseeseeseeecseeesceseesecsecseesececeaeesecaeseeeseeeaeeseeaeeaeseeeeeeeeaees 98 Searching for Motifs listed in a Databasen niie iieii it E A E ERA R RAER 98 Searching for a specific sequence Motif sissioni iani ee EEK EEA S E EE 98 Displaying a List of Search Res lis n ninnan a a E Sad cto A E A E ERA E 99 Adding a Mott Databases a A S 99 Browsing the Detail of the Found Motif cece cece sees cseeeeseeseecseeecseseeecseecsesseeesseeecsesaeeesseeesseeaees 99 3 15 Mutation Site Search 0 0 0 cece cc cece eeeceeesneeseeeeeseceeessaesesneeseseeessaesesaeesesneeseneessseseneeseenes 101 Explanation of the Result Window 101 Selecting a Codon Table 101 Selecting a Restriction Enzyme 102 3 16 Hairpin LOOp Search ni danaa ia eet ceed eunana aaan aaa naa rakaa aaa ai aAa amaaa Anaan 103 Explanation of the Result Window cceccscsssesseseeseeeeseceeceseeseeseesecneceeeaeeaeeseceeeeeseceaeeseeaeeaeeeeeereeseeas 103 Display ne a Tastior Search R OSL S 0s AA A aS os 103 Setting PALAMCLSS ese accu rar Ee PS ee cca RR E E ERE R E E ENE ER RRE E E 104 3 17 Stacking Site Search ccccccccec ct cetecedceweseee cece sceciewe sted ANNANN A KAANE NAAR REANA EAn 105 Explanation of the Result Window c cssccscsssssssssessesscssseccsscssceesersenscssessseeceneseescessencenseaesese
219. ence With a range selected The selected range is replaced with the content of the Clipboard Any characters invalid as DNA sequences and amino acid sequences are automatically removed before the paste takes place Selecting the Range If you drag part of a sequence using the mouse the color of the dragged area changes This highlighted area is called a selected range The selected range lets you perform a variety of operations including deleting replacement changes between uppercase and lowercase characters interconnection with the result of analysis and annotations Chapter 2 Refer to About the Target in 2 9 Editing and Analyzing Multiple Sequences Refer to About the Target in 2 9 Editing and Analyzing Multiple Sequences DNASIS Basics 31 10 20 30 40 50 Poe E EA E E E A E y ttgggggcga cactccacca tagatcacte cectgtgagg aactactgtc 60 70 80 90 100 eS eee ee ee eo ttcacgcaga aagcetctag ccatggeett agtatgagte ttetecagce 110 120 130 140 150 ele ee EENE N EEEREN EENE A S tccaggtccc ccecctcccgg gagagccata gtggtctgcg gaaccggtga 160 170 180 190 200 orererersrerarara Gaarererarerarararara saaa Raarerararararararara laarerararararararara 9 gtacaccgga attgccagea teaccegetc ctttcttgga tcaacccect 210 220 230 240 250 caatgcctgg agatttgggc gtgcccccgc gagactgcta gcecgagtagt Ways of Selecting a Specific Range There are several ways of making selected ranges
220. ence View right click in the result of primer design and select the Show Result List menu For the primer design result in sequence view select the sequence name and analysis name then click the Result List Dialog button A window that indicates the list of results of primer design appears ioj xi File Edit He u a gt ala No Kind Start End Length Te ect Any 3 Sequence Pi lett ZiT 2890 20 60 068 60 000 3 00 9 00 facocectecttttctaagca Riet 2785 2774 20 68 678 60 000 4 00 0 00 ecectatanccacet tcc Product 2671 2774 208 aceccctoctt ttcteagcaccatgantaaxcal eatereeacttae Pair 5 00 0 FIT Left 2570 2589 20 60 068 65 000 3 00 2 00 jeacoscstocttttetaage Rist 2755 2774 2059 879 50 000 4 00 0 00 jcccetataaccacstttcca Product 2570 2774 205 icaccoectoct Ut totaagcagvateaataaccateateetenctte Pair z E 3 00 1 00 Fo Left 2569 2508 20 59 327 65 000 3 00 8 00 jccaccesctecttttotaae Right 2755 2774 20 9 679 60 000 4 00 0 00 cectataaccacetttcca Product 2583 2774 206 icoaccecet colt ttct aagcascal enalaagcalzatezezactt Pair 3 00 00 ie Lett rear eso a0 69 393 45 000 3 00 0 00 actetooaascencenaaaa Richt 1739 i818 20 59 911 60 000 6 00 2 00 ecacetttecaactetccta Product 1631 1618 188 i agtet ccnazceaceanaaasaatettttaatattUgcangcanctt Pair 5 00 m5 lett 2571 2590 20 60 068 60 00
221. ended Dis BssNAI GTAITAG 6 blunt cut Show Selected FES BssSI CIACGAG CITOGTG 6 5 extended Oih BssTII CIOWWGG 6 5 extended Show Checked OSS Bst11071 GTAITAG 6 blunt cut CIACGAG CITCGTG 6 5 extended a aE colwaa 5 Stextended Lise Bst4Cl ACNIGT 5 3 extended Help OS Bs GCAGCNNNNNNNN INNNN ANNNNNNNNNNNNGS 17 aa 7 i Cancel Restriction Enzyme Database Manager 2 The Restriction Enzyme List lists the restriction enzymes registered The Enzyme Name with a checkmark specified in the check box on the left is the selected restriction enzyme Select a restriction enzyme that is searched for in the mutation site 3 Click the OK button Chapter 3 Details of Analysis 103 3 16 Hairpin Loop Search Searches and displays the results of hairpin loop position for a DNA or RNA sequence selected from the sequence editor Explanation of the Result Window Be Ek seo Yew teb JD SQ HR Ho SRAD I AAR BlESE Lt 2 S vow sian Sn e 3 Fe A tole n EPa Dsg aj Wio Probe Deia ffen e wre Su hip tilt tawh A Conner Volt Seach I im F Map View Ki Musia Sro Seas Eig 52 Sacks Sd Sere TA Tardi Rapeel Serch Pape Aw cove egtocceget ggyee qgs LORO CEGO 9 Sy bea eres manii rece Sequence View N Haphinpisi Hapide lt Hupo Heeyotoopt Hagako 2 FA E Target wer ekaa zis zia be fam a ae cimbamnintadnininininininiennininininininin cc gggcegessg teggeggt Heirpindoop
222. ength is 20 000 For example if displayed in Sequence View as below it will be converted into FASTA format as below In this case the number of characters is 38 Sequence View 10 20 30 0 30 w Eea a a DNAD0I Sequence aatigece NANI Sequence atecatec After conversion to FASTA format 170 Details of Analysis gt DNAQO1 aaggt tcc gt DNAQO2 at gcat gc If the upper limit error dialog appears in multiple sequence view decrease the target sequences refer to Select Target Sequences in Homology Search of 3 44 Searches Using GeneIndex and try Homology Search again Motif and Domain Search Use amino acid sequences to perform GeneIndex Motif and Domain Search When using this search a sequence that displays in DNASIS MAX will appear in the search string of the Motif and Domain Search It is possible to specify other conditions then perform the search Select Target Sequences The sequences that display in Sequence View are the target in the Motif and Domain Search You will have to hide sequences you want to remove from the GenelIndex search target 1 Enter a new sequence or import one from an existing file 2 Click from the View Toolbar to switch to amino acid view 3 To remove a sequence from the search right click over the sequence name 4 Then select Hide from the popup menu The sequence will be hidden and only the search target sequences will display in Sequence View Select Species Select a targe
223. ent J amp o Ee gry arre hoe eter trey ewyre Fie nerve Qpen Filton Aetcton Enzyme Fies engme Cancel Select a file storing restriction enzyme data and click the Open button DNASIS imports restriction enzyme data while performing format checks Format Error dialog box If the restriction enzyme being imported contains a format error the Format Error dialog box appears DNASIS cannot import a restriction enzyme which contains a format error This enzyme have format error You can not import this enzyme Skip All Cancel The following describes the conditions which cause a format error Check the format of the data you are importing Conditions causing a format error 1 The Normal text area does not contain a recognition sequence 2 The Normal text area contains a character other than ACGTURY WSKMBDHVN and 3 The Normal text area does not contain an exclamation mark or it contains more than one exclamation mark 4 The Complementary text area contains a recognition sequence including a character other than ACGTURY WSKMBDHVN and 5 The Complementary text area contains a recognition sequence without an exclamation mark or more than one exclamation mark 6 The Complementary text area contains a recognition sequence having a length different from that of the sequence in the Normal text area Button description Button Description Skip button Skips the restriction enzyme which contains
224. equences Smith Waterman Search Explanation of the Result Window Refer to the Explanation of the Result Window in Section 19 BLAST Search Selecting a Database to Be Searched Smith Waterman search only 1 Click the Smith Waterman Search icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a GENE BRIGHT III Parameterset Editor will appear 2 In the Target Database field place a checkmark in the check box for the database you want to search through Calculate by Sottware E multon hps Segane Type amen a F Matr t eLosums a Ftal Gap 5 al Ertention Gap H Mar than ot Return E D Oa Of Score Tareet Database JMSK h fonsi eHow PIR foou wht Select All Deselect AI 3 Click the OK button 158 Details of Analysis 3 39 Multiple Alignment Amino Acid This function performs multiple alignment or optimum alignment of multiple sequences using multiple sequences that have been entered by the Editor The algorithm used here is Clustal W Explanation of the Result Window Refer to the Explanation of the Result Window in Section 22 Multiple Alignment Setting Criteria for Determining Match Bases The result of multiple alignment is color coded according to the match rate You can change the match rate and color combination 1 Click the Parameters icon on the toolbar to open Sequence Editor Parameter Set Editor 2
225. er screen click the New button 2 The New Vector dialog box appears 3 In the New Vector dialog box click the Import button 236 Databases 4 Select the external definition file to import and click the Open button New Vector x Enter New Vector Name Type of Vector Circular O Sequence f Import ry Accession Definition Features Features Start End Add a Items imported from an external definition file You can search the external definition file for several keywords to import the values defined with those keywords Table 3 shows relationship between keywords and the items to be imported Table 3 Item Required Import Keyword Enter New Vector Name x Type of Vector x x Searches for the external definition file for the keyword LOCUS Imports the item in the Circular mode if it is defined as Circular otherwise imports the item in the Linear mode Sequence x x Searches the external definition file for the keyword ORIGIN Imports the lines up to the line as the Sequence Definition x Searches and imports the external definition file for the keyword DEFINITION You can define more than one DEFINITION Accession x Searches and imports the external definition file for the keyword ACCESSION Features x Searches and imports the external definition file for the keyword FEATURES You can define more than one FEATURES Reference x Searches the e
226. er setting and may allow the default settings to be edited by you Examples include database selection for homology search enzyme type selection for restriction enzyme search and codon tables for translation Use the following procedures to carry out such parameter based analysis 1 Click the relevant analysis button 2 When the Analysis dialog box appears click the Parameter button 3 The parameter setting dialog box appears This is different depending on the type of analysis 4 Set a parameter or parameters 5 In the dialog box click the OK button to close the dialog box Redoing Analysis After for example editing sequences or changing parameters you may want to redo the analysis In that case use the following procedures 1 Click the Analysis button again 2 When the Analysis dialog box appears click the Execute button The following dialog box appears In response click the Overwrite button The analysis Translate of sequence Tutonal3_1 aleady exist What do pou wart to do 3 The result of analysis is overwritten Ifyou click the Add button in step 2 instead a new result of analysis is added to the display Deleting the Result of Analysis You can delete the result of analysis in the following way 1 Left click the analysis name for a result of analysis you want to delete Once you left click to select it the analysis name is underlined as shown in the figure Sequence TGTNAGGT Tra
227. ers 4 13 Motif Search el Nuc leic Acid Motif Search Parameter Set Editor IV Use Motif Database J Use Input Pattern D I Search Complementary Sequence Help Item Use Motif Database Check All Uncheck All Setting Cancel Description Select this check box when using a motif database If this check box is selected you must select at least one motif database You must select either or both of the Use Input Pattern and Use Motif Database check boxes Motif Database list A list of the motif databases registered in the database Select the check boxes of the databases you want to search Ifthe list does not display any motif databases click the Setting button to start the Nucleic Acid Motif Search Database Manager and specify the directory containing databases Use Input Pattern Select this check box to search for a motif using an input pattern If this check box is selected you must enter a pattern You must select either or both of the Use Input Pattern and Use Motif Database check boxes Input Pattern text box Enter a search pattern when searching for a motif using an input pattern Search Complementary Sequence Select this check box if you also want to search for a motif for a Complementary sequence If this check box is cleared DNASIS will only search for a motif for a Normal sequence If this check box is selected DNASIS MAX will search for a motif for both Normal and
228. eseeseceeeeseeeeeeeseeneeeees 11S Selecting a Database to Be Searched Smith Waterman search only cece eseeeeseeeeseeseneeseeeeeeees 115 3 22 Multiple AlignMe mt ci c0 fsceccecviececectacetesevecececcetadectesssiesectucnredevscecesceusdersu asuesecausereteesuere erezee 116 Explanation of the Result Window ots acess css cazesca5s ea ca_h soz cesyesdsdeds ies ieahded sezies E AEE 116 Analyzing a Selected Range with Sequence Analysis Tools 0 cccceceeeseseessescseeseescseeeeseeseeeeseeeeeeaeees 116 Meaning of the Background Color and How to Change It oo cee cceeseeeseeseeecseeecsesseeesseeseseeseesaeees 117 Editing an Alignment Sequence wo eee eeeseeeeeeeeee 117 Changing the Order of Sequences Choosing Sequences in a Project that are to be Aligned 117 Alignment after Masking Regions within Sequences ccescescessesseeseeseeseeseesecsececeseeseeaeeaecaeeneeeeeeaeeaes 118 Creating a Cons nstis Sequence iis iassstezseessbiccsszavecerastincas a A RAE EAEE TEE IEE ETATER ASES 119 3 23 Phylogenic Tree DNAj icc ccccscececescetscessuececceucdeceevasceterusceeecevstececcuacdectevssaetectadnceiedsnerevertzae 120 Explanation of the Result Window Changing the Type of a Phylogenic Tree Changing the PON a r cess tie tes a hand eee vabbe ceabiac aah lanes e testbeds A Displaying a Magnified Phylogemic Treez 0 0 lt 2secescescexsascnccesteascexeatatccecsoenccreanandiersuaceessoa roveesyeanteesaearoieves
229. esesssssssstststssststsrrssssrrsnrtntsestsrstseeesrsrsrsts 33 Changing Analysis Parameters isser pei aE EEan ASE TE SEEE EiS EEE SEVES EEEIEE SVE RSE 34 Redoimg Analysis e R E E N ER 34 Deleting th Result of Analyseer ieia E EE A EE 34 Hiding the Result of Analysis eeii rae a E EEE EE A E A RERS 34 Redisplaying the Result of Amalysis cccecceccescessesseseeseceecesceseesecsecsececeeeeaeeseesecseceseseeaeeaeeaeceeneeeeseaees 35 2 6 Customizing Display Of SEQUENCES ccccceeeeeeeeeeeeeeeeeneeeeeeeeeeeeeeeeeeeeeeeeeeeeseeneeseeeseeeeeeeenenens 36 No Bolding Back Characters tc sc cGsi ion itues aes seca A A A E 36 Folding Back Characters According to the Window Width oo icici ssceecseeseeeeseeecseeececaeeetseeeeeeaeee 36 Folding Back Characters According to a Specified Width Inserting Spaces after a Specified Number of Characters Block Based Display Mode eee 37 Hiding the Raber a cuncadvennescevsouscanteaneznedsvencesevaitedlsuavercessunbetananvercuneen 37 Ways Of Displaying the Ruler m sc sca coves cas niorir e EEE E A REEERE ET 38 Changing the Font for Sequences lt 0 sesira seiri EE E EEEE E EE E EAEE ERE ERE ENEE ES 38 Chanemig the Colorof Sequences i ora er SEa E EEA EA AE A R E AEE AA 39 Displaying Pre Edit Original Sequences s 3 5scs s ccsessccessedeesavssssacassessicssosunveasseasssoeusevesneseuuasneesvoa sescsube se 39 Displaying Complement Sequeiicess S rns a beaecie baer oents iene tiaisen dias 39 2 7 E
230. essssnusssscessssuussesesesssnnesseeessnsneeeesee Summary of the Parameter Set and Description of Each Parameter s s sssssssssssssecssssssessecessssneeeess 231 5 4 Vector Database isinisi aaan aaeain arana ianen ie aaa inaani iwa daadaa 232 Window Deseript Oi iie aSa n EE OEE EE ERATE ESE ea heater anata 232 Contents Xi Cr ating a New Vector ccccdaiceevectesvndesvncenniateimn glenn dana Ga AE CERNE TAEKE AE 232 Modifying Vector Informations aerie ae erea AEE EEA EEE aE e R 233 Modifying a Cloning Site ersen uaaa Ea E EE E E E E E ER 234 Modifying a Featut escerai rire a a NE E ERNE NERONEN ONTOSENA 234 Deleting amp Vector iis pesisesc sorso ursii rosa aar ASEE EE AAEE PESEE EEEE TEPEE EERS SEEE SIPE IE eias 235 Displaying References ecceccesceseeseeeeeeeeeseeseeneens a233 Importing a Sequence from an External Definition File we 235 Importing a VeCtor orreee eie E RS 238 Exporting a VECtON raea En EAE AEE RENAE vous E E EEEE EE AE OAE RA 238 5 5 Amino Acid Motif Datab Se assassiner enee inp ioinronpen nupur oianean npase eiorinn buns ma sikur iian pdania ankins 239 Window Description esisin aint oa A EER E AEAEE ton Rest A EEEE SEE EEEE ETR i Editing the Contents of a Motif Database soises ner annann E R E E Displaying a List of Registered Amino Acid Motifs a Displaying Mouf Properties sissa asie sess aE E sescaves sees EAO EEEO TEES Adding a Motif Database soiien a EN S 5 6 Restrictio
231. ette cge gegtct geo t tg g tgtogtgc Sequence tette cge gegtct goo t t tg g tgtegtge Sequence tette ege gogtet goo t tag tgtegtge Sequence tette ege gogtet geo t tg g tgtegtge 10 wo 10 AB016785 Sequence ceceectece ggg g gcc t gtggtctg cgg coggt ggt oc ABO31663 Sequence ececectcee ggg g goo t gtggtctg cgg ccggt g gt Cc Cay Target AF011753 Position 1 bp Num A Ifa file used for import has multiple entries an entry dialog box will appear where you can import only the entries that you want File Name VES OS n iaaa tet Skip This File Total F entria Seketed PT entria Item Description File Name Shows the name of the currently imported file Total Shows the total number of entries contained in the currently imported file Selected Shows the number of currently selected entries Entry List Shows the entries extracted from a multi sequence file An entry with the checkbox on the left selected is an import target Up to 20 entries appear in one window Previous button Click the button to show the 20 entries before the entry currently shown in the list Next button Click the button to show the 20 entries after the entry currently shown in the list Select All button Selects all entries Deselect All button Unselects all entries 28 DNASIS Basics Refer to Renaming Sequences in 2 4 Editing Sequences basic Help button Opens the online
232. etting gcateta cctce Ruler Displays the ruler Use the ruler to obtain rough measurement You can move the ruler 1100 vertically by gripping the ruler line using the mouse ee ee ee a Ow war wa gcatgta cctcc 80 Details of Analysis 3 9 Vector and Low Quality End Trimming This function searches DNA sequences for low quality end portions and vector sequences It also displays the region where the low quality end portions and vector sequences have been trimmed Explanation of the Result Window Ge GE jome n ied OFU PEBAA detan Aaaa ti oe ELEAL E OMA Base Map View Sequence View AGGLADC CACKRUGTTTY TOTTSCAOGE ATITAATITA TATTOCACCC Sequence View This view displays the result of trimming according to the preset conditions below the sequence It displays the following Trim Always Shows the region that has been unconditionally removed from the end irrespective of the quality or vector sequences Low Quality Shows the region that has been removed because of low quality Vector xxxx Shows the region that has been removed as the vector sequences Trimmed Sequence Shows the region from which the vector sequences and the low quality region have been removed Trimming Only Vectors In the initial setting both the vectors and the end are trimmed You can change the initial setting to trim only the vectors 1 Click the Vector amp Low Quality Trim End
233. ettings In Internet Explorer select Tools gt Internet Options from the menu Click the Connections tab then click Settings for Dial up connection or LAN Settings for LAN connection If there is no check in the Use a proxy server for this connection or Use a proxy server for your LAN check box you do not need to change the setting Ifthere is a check in the box check the Use Proxy Server item in DNASIS MAX and fill in the Server and Port information with the corresponding information in Internet Explorer If there are advanced settings click Advanced in Proxy Server of Internet Explorer and use that information Only when the Proxy Server requires user authentication fill in the User Name and Password items You should leave these items blank if there is no need for user authentication 286 Tutorial 7 2 ORF Search This section deals with searching for Open Reading Frames ORFs It also demonstrates searching for motifs in amino acid sequences that are generated by translating ORF data This section examines the following operations Starting DNASIS MAX Entering the sequence e Searching for open reading frames Translation e Searching for amino acid motifs 7 2 1 Starting DNASIS MAX After clicking the Start button in Windows select the following Program DNASIS MAX and then DNASIS MAX Alternatively you can double click the DNASIS MAX exe icon ep in the DNASIS MAX installation destination fol
234. ew Page Setup Makes a printer setting Print Starts printing Exit Closes the window Edit menu Description Undo Cancels the previous operation Cut Cuts the data Copy Copies the data Paste Pastes the data Select All Selects everything Find Attempts to find the target Find Again Attempts to find the next target View menu Description Navigation Toolbar Toggles the Navigation toolbar to display or hide it Format Toolbar Toggles the Format toolbar to display or hide it Status Bar Toggles the status bar to display or hide it Data menu Previous Data Description Displays the previous data item when multiple items are opened at the same time Next Data Displays the subsequent data item when multiple items are opened at the same time Chapter 3 Details of Analysis 135 Data menu Description Sort Sorts all data item in ascending or descending order Help menu Description Contents Opens the Help About Grid Viewer Displays the version Button Description W Export button The same function as the Export menu Print button The same function as the Print menu Cells Query Dataname Shows the name of a query sequence Target Database Shows the database that is the target of BLAST search Sequence ID Shows the ID of the entry in the original data
235. f an analysis PUG DNA Toolbar Icon Function Adds DNA sequence Ss Shows a translated amino acid sequence that was selected in DNA sequence view in amino acid sequence view Converts into a reverse complement sequence Converts into a complement sequence Converts into a reverse sequence Converts the expression of a sequence into uppercase characters Converts the expression of a sequence into lowercase characters Converts the expression of a sequence with uppercase and lowercase characters Masks the specified or highlighted stretch of sequence JS oo es SNe de 14 Searches a sequence Moves the cursor to the specified position on Amino Acid Toolbar Icon Function Adds an amino acid sequence Converts highlighted or entire sequence into uppercase characters DES Converts highlighted or entire sequence into lowercase characters Converts highlighted or entire sequence to opposite case characters Masks the sequence of a range L a Searches for a specified sequence string id Moves the cursor to specified position Chapter 1 Window Descriptions 7 Annotation Toolbar Icon Function Adds a new annotation Adds an annotation entry Adds more than one annotation entry at the same time ISS Adds a part to an annotation Moves the selected annotation or part one step up
236. following window appears H Save in lt j My Document eD cr EJ My Pictures Save at type Space Fike maprotie Carcel 5 Specify the names of a folder and a file you want to save and click the Save button Import Procedure 1 Click the Create Multiple Alignment Profile analysis menu and an Analysis dialog box Then click the Parameter button 2 Click the Profile Manager button to display the Multiple Profile Manager 128 Details of Analysis 3 Click the Import button The following window appears ajMy Pictures cs Fies of ype Mubiple Algrmert Proties maprotile Cancel l 4 Specify the name of a file you want to import and click the Open button The imported profile is displayed in the list of the Multiple Alignment Profile Manager Chapter 3 Details of Analysis 129 3 26 Using Phylogenic Trees Profiles DNA This function creates a phylogenic tree by adding a single sequence to a multiple alignment profile that has been produced in advance Analysis Procedure 1 Click the Phylogenetic Tree using profile icon from analysis button view and an Analysis dialog box will appear Then click the Parameter button Make Multiple Mignment Profile Parameterset Editor Sa x Gererel PaimiceAbernent MultipeAlierment Proteinep Tree Profde Nare EST NA Sequence Type paa Quta Order Oder by Aigre I Lee FAST Aleorithen tor the alen mart Protein
237. from line 2 to the point immediately before a line beginning with is read as a sequence Line 1 ranging from the point after gt to the end of the line serves as a sequence name and a comment Any sequence including a character that is not found in DNA sequences is regarded as an amino acid sequence otherwise the sequence is regarded as a DNA sequence If sequences are separated by a line in a file all of those sequences are read as one Reading Files in the GenBank Flat Format This is a standard format for the GenBank Database The part of the Sequence record ranging from the LOCUS line to the point immediately before the ORIGIN line is displayed as a comment in the Comment view pane The part ranging from the point immediately after the ORIGIN line to is displayed as a sequence in the sequence view pane The first accession number in the ACCESSION line is used as a sequence name If there are no accession numbers the LOCUS name is used as a sequence name Ifthe LOCUS line includes aa as the sequence type it is regarded as amino acid FEATURES are displayed graphically as annotations If sequences are separated by a line in a file all of those sequences are read into and displayed in one project In this case a dialog box titled Import List will display the list of individual sequences allowing you to select those to be imported Reading Files in the EMBL Format This is a standard format fo
238. h and non match By default yellow is for 100 matches green for matches of 51 or more and light blue for matches of 50 or less The portion in a red frame in the Map View is displayed in the Sequence View Example of Calculation Time The following is an example of calculation time without using bootstrap on a Pentium II 550MHz machine Average Number of sequences sie length Analyzing a Selected Range with Sequence Analysis Tools In the alignment display mode you cannot directly perform other types of analysis To carry out sequence analysis on regions of sequence based on multiple alignment view perform the steps below 1 In Alignment view select a region you want to analyze as shown in the figure Chapter 3 Refer to Changing the Order of Sequence Display in 3 22 Multiple Alignment Details of Analysis 117 M00001 Sequence mo0002 Sequence M00003 Sequence M00004 Sequence zccagcccce tgatgggggc gacactccac catgaatcac tecectetea ggaactactg tecccgccce taaatggggc gacactccec catgaatcac tecectetea ggaactactg gccagcecce tgatgggggc gacactccac catgaatcac tecectetea ggaactactg gecagcecce tgatgggggc gacactccac catagatcac teccctgtga ggaactactg 70 80 90 100 110 12 M00001 Sequence mo0002 Seguence M00003 Sequence M00004 Sequence tcttcacgca casagcetct azcateece btastatzas betcetecas cotccaczac tcttcacgca gaaagcgtct azcatesce btastateas betcetacas cotccazsect tcttcacgca gaaagcgtct acOGa
239. h the same value Search and j Extraction IV matching percentage is more than fs and overlapping sequences are more than fico and I score is more than 300 and MV E value is less than 01 and I7 overlapping length for query length is more than 95 I Output header line J Output query sequence m o 3 Set the extract conditions 4 Click the OK button to complete the setting Chapter 3 Details of Analysis 137 3 30 Amino Acid Content This function analyzes amino acid sequences and displays the result of analyzing the amino acid content Explanation of the Result Window A AKS7570 AminoAcid Basic Analysis Eie Edit View Help F jAAko570 Aminoscid Usage 1 Totel_Amino The number of Awinofcid 2 Molecular Weight 23911 95 2 Aminodcid Count Yo Percent Ala a 3 Are R 3 27 AsniN 4 23 Asp D 3 Cys C 0 Gin Q 2 1 Glu E 2 Givi 20 7 4 Hie H 2 29 Tle T 7 LeulL 3 7 98 5 Lys K Het H Phe F Pro P Ser Thr T Troit Tyr Val Asx B Gix Z mene Kxx K BSOOCCSOIMS SOmMnNwwS w 6 Ready 1 Total number of amino acid residues 2 Total molecular weight 3 Molar ratio 4 Number of amino acid residues 5 Amino acid name 6 Total molar ratio File menu Description Export Exports the data in the window into a text file Print Prints the window Print Preview Displays
240. he range of a match is indicated by the numeric value at the top of the bar Subject Part Bottom of the window One sequence corresponds to one bar The numeric value at the rightmost of the bar indicates the sequence length A match is displayed in the color corresponding to Score A shaded part represents a complement sequence Ifa single sequence contains more than one match the same bar displays these matches The highest match in terms of Score is aligned with the Query to serve as the reference position Each of the other matches is displayed in a relative position from the reference position The gray bar indicates the correct length The white bar indicates the length longer than the window by fixing the width of non matching parts Alignment View Displays all alignments Double click the icon on the left of the sequence header to obtain the sequence s GenBank Report and add it to the DNASIS Main window The background of sequences in the selected status is displayed in the Windows based color Chapter 3 Details of Analysis 111 Shows the Match sequences between Query sequence and the Subject sequence BLAST searches for protein translation and amino acid databases Item name Description Parameter name Type Shows the original database where the subject sequence has been registered gb GenBank emb EMBL dbj DDBJ etc ID Shows the ID of the entry in
241. he selected profile name that profile will be overwritten You cannot select a read only profile The gf icon represents a DNA sequence profile while the HH icon represents an amino acid sequence profile Profile Manager Opens the Multiple Alignment Profile Manager You can create delete import and export a profile or modify the attributes of a profile Sequence Type DNA or Protein is automatically selected depending on the type of the selected profile Note Clustal W can process both DNA sequence data and amino acid sequence data This parameter causes Clustal W to handle the input sequence data assuming it to be either a DNA or amino acid sequence If this parameter is set to DNA inputting amino acid sequence data as determined by DNASIS MAX results in an error and the sequence is not processed Output Order Corresponds to the outorder parameter of Clustal W You can select either Order by Aligned or Order by Input with which the value aligned or input will be set respectively Note This parameter specifies the order of the input sequence data within the result output from Clustal W If you select Order by Aligned DNASIS MAX will output the results arranged in the order in which they appear in the guide tree or phylogenic tree If you select Order by Input DNASIS MAX will output the results arranged in the order of the name of the input sequence data Use FAST Algorithm for the
242. help Changing the Frame 1 Click the Translation icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear Chapter 3 Details of Analysis 77 2 Select a frame in the Start Position field in the Codon Usage window as shown in the figure Codon Usage Start Position 3 Click the OK button 78 Details of Analysis 3 8 GC Content This function calculates and analyzes the percentage of G or C that is included in every 10 bases of a DNA sequence The result of analysis is graphically shown in another window Explanation of the Result Window d DNASIS Be k pamo pe Hb Herd gt BE GQ4O 72 27 48 454 ss tee ii oe eR ESE Ds Ow as UNA Bose Map View Sequence View Map View This view displays the graph of the entire sequence on the bar Sequence View This views graphically displays the result below the sequence Customizing the Result Display If you right click in a graph a menu is displayed This menu is used to customize the form of graphs 680 690 700 besecescaa cagcatesce agcesestce Line Graph 3 v Plane Graph Fecaggacca gctgggctac cegcagcace q Menu Function Line Graph Displays the GC content in a bar graph 80 t tecttttza Chapter 3 Details of Analysis 79 Plane Graph Displays the GC content in a histogram This is the initial s
243. help Import button Click the button to import the selected entry into the sequence editor and close the dialog Skip this file button Closes the dialog without processing the current file Cancel button Closes the dialog without processing the current file All subsequent files are also not imported About the Sequence Name Any sequence that has been read from a file is automatically given a sequence name For the naming rules refer to the description of the reading of different file formats into DNASIS Be aware that sequence names involve the following restrictions Characters that cannot be used Japanese Kanji and Kana characters and the following characters lt gt Length Up to 128 characters a alta of po amp ose ee anise gt 448 tAbtere em 2 hnar gt Owi em i m m r FE l JDA fa o E or H w 5 ML ee leper orate ete wok emt mena oon ee Aa paee Cone p noah tep or e i Invalid characters for the sequence name are changed into A string exceeding the limit of 128 characters will be truncated to the limit It is also possible to change sequence names manually The following dialog box appears when there is an attempt to read another sequence of the same name The sequence AFO87301 already exist What do you want to do Add Cancel Cancel All Overwrite Overwrites the existing sequence Add Automatically ch
244. his area is blank Normal text area A text area used to enter the recognition sequence for the restriction enzyme you want to create Enter the recognition sequence using a complex code containing characters from the string ACGTURY WSKMBDHVN not case sensitive Enter an exclamation mark at the position to cut Specify the characters in the direction from 5 to 3 Complementary text area A text area used to enter a complement recognition sequence if the restriction enzyme you create does not have a palindrome structured recognition sequence Enter the recognition sequence using a complex code containing characters from the string ACGTURY WSKMBDHVN not case sensitive Enter an exclamation mark at the position to cut Specify the characters in the direction from 5 to 3 Text area for the number of bases Automatically filled with the same length value of the Normal recognition sequence excluding an exclamation mark If you enter a recognition sequence in the Complementary area it must have the same length excluding the exclamation mark as that specified here Combo box for the Kind of Cut Automatically selects the cut shape for the restriction enzyme For details about the cut shape refer to the description of the Restriction Enzyme Database Manager window OK button You can click the OK button to register the new restriction enzyme created This button is disabled if DNASIS detects any of the following erro
245. hondri 272 e 0 Cervus nippon nippon mitochon 263 4e 071 __ 8 RF036275 AF036276 Tragelaphus euryceros cytochr 264 7e 070 3 By L01544 ODOUTRHC Odoooileus hemionus hemionus 262 3e 069 7 3 5 Using the Editor to Enter the Highest Homology Sequence as a New Sequence from the Search Result Window From the result list select the hit with the greatest similarity ID M98484 AALMTCYTOB and click the Get GenBank report button Ee on the toolbar Eile Edit Heb a B Score 1 very CE DNASIS Max will then attempt to acquire a file with the M98484 accession number in the GenBank format via the Internet using the Entrez system at NCBI If the attempt is successful this sequence is added as a new sequence to the Editor 294 Tutorial oe oma oe oF er eee Coen te 8 ES Se Ele ees Peel Ty ee 232 betnas 7 3 6 Running Multiple Alignment After selecting the DNA Multiple Sequence group on the analysis button bar click the Multiple Alignment button and an Analysis dialog box will appear Click the Execute button An alignment between two sequences using the ClustalW method is performed with the result being displayed in the Editor Fen oe y oe SS E es jose POF GR AST 48 BIB Sete vers zane vanni DsBnas OCR aa CTA0COGOGT bruger CraTTaaeec eeapaeneet eeneeaeent eeneeeanet eneereennt eanenannnteenenaa Cantecatts Tacactoea staatascas CATION fercsctec TOGOG CASTECATT
246. icon and an Analysis dialog box will appear Click the Parameter button and a Parameter dialog box will appear 2 Click the Trim End checkbox to uncheck it in the Parameterset Editor window as shown in the figure Chapter 3 FF Trim End F 5 ENO I Trin at bast i F Trin the first 10 tp mhite the quality is kas than 0 s F 7 ENO M Tren a ___ Fite o pai thor E F Same as amp END pBluescript 53 select your clorung site Gf you Mant to choose double cloiing she select with Ctrl Key Windom size for vector timning a t Minimum Matching Percentage considered aa contamination 60 w Output optiona IF the sequence length is kss than 12 bp output to I Others folder I vecie kimning length is 0 be output to Others folder I Out trimmed seqerce at N Vector DB Nenoeer Defsult Cancel Heb 3 Select the vector you want to trim from the Vector name list in Trim Vector Details of Analysis 4 Select a cloning site You can select up to two cloning sites by pressing the Ctrl key 5 Click the OK button Registering New Vectors 81 In addition to vectors registered in DNASIS in advance you can register new vectors for trimming in the vector database 1 In the Analysis Button View click the Database tab and then Vector Database to open the Vector Database Manager window 2 Click New at the bottom of the Vector Database Manager window to display the New Vector window as shown
247. if the database is locked Cancel button Discards all changes and closes the dialog box Adding a Motif Database 1 In the analysis button view click an amino acid motif database 2 Click the New button in the Amino Acid Motif Database Manager as shown in the figure DNASIS creates a database Untitled in the window ia PROSITE Release 13 Untitled DB Path 3 Click the Untitled database to highlight it 4 18 CO kook 9 25 4 Click the Property button The Amino Acid Motif Database Property dialog box appears Make necessary settings 5 Click the OK button Chapter 5 Databases 243 5 6 Restriction Enzyme Database You can display a list of restriction enzyme databases DNASIS MAX supports the functions for creating editing deleting importing and exporting restriction enzyme data Window Description The Restriction Enzyme Database Manager consists of the main Restriction Enzyme Database Manager window the New Enzyme window for creating new restriction enzyme data and the Enzyme Property window for editing restriction enzyme data Restriction Enzyme Database Manager window This is the main window of the Restriction Enzyme Database Manager Parameter Description fic Rest tion Enzyme Database Manager 4 Name Recognition Sequence Bases Kind of Cut ApaLI Apol Ascl Asel AsiAl Asnl Asp 7001 Asp 181 GITGCAG RIAATTY GGICGCGCO ATTAAT AICCGGT ATITAAT G
248. in an in house database Selecting a Destination Database 1 Click the In House Database Registration button either DNA or amino acid and an Analysis dialog box will appear Click the Parameter button and a Sequence Database Updater Parameterset Editor will appear Sequence DB Updater Pararmeterset Editor I Empy databace belote updating Source Data In house tasta Update misted blast database atte updating F Make new bist database d does eist Hame tot Seqe Date Comment Ww PR 29704 2001 8 3 The database is derived trom the rH oN a WF In Houe ti s 2001 10 11 P Example 0 2001 11 16 2 The Select target databases field shows a list of databases Click to highlight the database to which you want to register a sequence 3 Select OK Registering a Sequence in the Database 1 As explained before select the database to which you want to register a sequence 2 Click the sequence on the sequence view 3 Click the in house database register button Creating an In house Database 1 In the analysis button view click the sequence database button The DNA Sequence Database Manager appears 2 Click New in the DNA Sequence Database Manager screen The New Database dialog box appears 3 Click the in house tab 4 Make necessary settings for the database to create and click the OK button The following table describes the items on the screen Name Enter the name of the data
249. ing or displaying DNA sequences click the 4 button on the View Toolbar To switch to the mode of importing entering or displaying amino acid sequences click the EA button on the View Toolbar 24 DNASIS Basics 2 3 Using Existing Files Opening Sequences from the Menu You can read sequences from an existing file 1 Select File gt New Menu and a prompt dialog will appear For Type select DNA and for Content select Sequence from files then click the OK button 2 This displays the file selection dialog box in which you can select a file or files you want to read 3 Click the OK button to read the selected files so that the corresponding sequences are added in the window 4 It is also possible to select multiple files and read them at once alaiz th pR gume Ben tb osu See 6A t OF 4282 26429 2 gt PS Pawan ove D Ree Refer to Reading Multiple Files in 2 3 Using Existing Files Opening with the Drag and Drop Method Using the drag and drop method you can read files using Windows Explorer 1 Set the DNASIS Main Window to DNA or Amino Acid mode depending on sequence file type 2 From Windows Explorer select a file you want to read 3 Drag and drop the file in the DNASIS window ee ais p p be oF oe ee gantqBe 42 gt 464 e20i 222 ee eetu ar iv Di Bem TA tal 3 Peen fs AF011753fsa D w FA Referto Qt S OO ad Reading
250. irus 3 MSP Human herpesvirus 3 MSP Human herpes Complete ods Human herpesv Human herpesvirus 3 MS cone complete ode Human herpesy SP ORFO ORF ORF47 ORFS ORFE2 ORF31 ORFET Mus musculus stran CS7BL 6 natural killer cell receptor Ly49M Ly49M mRNA cc Rattus norvegicus transient receptor potential Trp4beta mRNA complete cd Rattus norvegicus transient receptor potential Teptaiphs mRNA complete cds Escherichia coli florfenicol resistance protein Fio lo gane complete cds Bordetella bronchiseptica fimbrial subunn protein FimN Himn cene promoter and Description You can select the results by clicking them You can use the Shift or the Ctrl key to select more than one entry From the menu bar you can also choose Edit and then Select All to select all entries With an entry selected choosing Edit and then Copy copies tab delimited text data of the accession number and definition to the clipboard You can paste this data to MS Excel or other applications Column header Clicking the column header with the mouse makes it possible to sort data based on the column Another click on a key column toggles between ascending and descending order GenBank Report button Obtains the layout of selected entries The obtained data is added to the Sequence View New Search button Deletes all the current search conditions and enters new search conditions 166 Details of Analysis Search Within Results b
251. is Assa Part Cor Font Tab Item Select View box Description Selects a view for use in font setting Window Descriptions 11 Setting button Font Name Font Size Font Style Displays the window for font setting Indicates the font name Indicates the font size Indicates the font style Line Interval Sets the line interval Selected Range Pen Color Sets the color of the selected frame Selected Range Paint Color Sets the color of the selected range Emphasis Area Pen Color Sets the color of the highlighted frame Emphasis Area Paint Color Sets the color of the highlighted range Initialize Initializes all settings to factory presets Use as Defaults Store the current settings as the default settings Sequence Tab SS xj Foa Sequence Foking Fue l Show mand sequence T Show compdemertary saqen Magie Sequence Coby Backgouns Pestect match w F Machno 5 x EIJ T Core Saguen Back gound pu de J Drapia Mode G DNA C RNA Fosground od T Use Detaas Item Show original sequence Description Displays the pre edit sequence the sequence directly after reading from a file at the same time Show complementary sequence Displays the complement sequence of a sequence at the same time 12 Window Descriptions Display form of a sequence Specifies the type DNA or RNA of DNA sequence
252. isplayFontName Courier E DisplayFontSize f fa DisplayFontBold false C true DisplayFontltalic false C tue DisplayFontUnderline false C true 2 To change the font use the Display Font Name field To change the size use the Display Font Size field 3 Click the OK button to complete the setting The phylogenic tree under a new setting appears Displaying an Expanded Phylogenic Tree 1 Click the R icon on the toolbar The shape of the mouse cursor turns to a magnifying glass LEONo i 2 Click or drag any portion you want to expand The specified portion is expanded To shrink it click the Q button and perform a similar operation To return the display to its original size click the E button Setting an Out Group You can set the selected branch as an out group 1 Click the o icon on the toolbar The shape of the mouse cursor changes to the mark tl aaon m Wi Xe i 2 Move the cursor to a branch you want to set as an out group and click it The specified branch is now set in the out group Chapter 3 Details of Analysis 161 Replacing Branches You can replace branches 1 Click the G icon on the toolbar The shape of the mouse cursor changes to the mark E raon mu dG i 2 Move the cursor to a branch you want to replace with another within a tree and click it The specified branch is now replaced and displayed Evaluating the Branching Reliability Bootstrap Tree
253. l sequences amp PRI 95 550 1996 6 13 primate sequences P RNA 4 067 1994 4 27 structural RNA sequences amp ROD 45 950 1995 5 11 rodent sequences STS 75 253 1998 2 1 STS sequences sequence tagged sites w DB Path Make Cancel Item Description Name Displays the name of the database of Seqs Displays the number of sequence data items stored in the database Date Displays the date when the database was updated last Comment Displays comments if any Button Description DB Path Allows you to specify the path of the directory to store the sequence database Make Creates a dedicated database for BLAST searches from the database Cancel Returns to the previous screen 264 Create Plasmid Maps Chapter 6 Create Plasmid Maps Chapter 6 Create Plasmid Maps 265 6 1 About Creating Plasmid Maps It is possible to create a plasmid map of a selected sequence in Sequence View A plasmid map is represented as a circle with the name and length of the sequence located in the center Restriction enzymes are put on the circumference of the plasmid based on position Annotations are displayed using arrows based on the start and end positions lt _ Restriction Enzyme Sequence name SEAP_ Annotation S length equence leng a Plasmid maps can be edited by adding or changing plasmid figures such as restriction enzymes annotations and DNA or deploying normal figures su
254. l settings 200 Details of Parameters 4 19 Internet BLAST Search DNA and Amino Acid Internet Blast Search Parameterset R Sexon Sie TETEE URL fits Jormmencbinimntuecy blest Blastori So Sette Carcel Dotat Hep Item Description Search Site Name of the search site This version only supports NCBI advanced BLAST search URL URL of the NCBI site used in case the URL is modified Priority Specifies whether DNASIS will assume a sequence as a nucleic acid or amino acid sequence if it cannot determine the acid type from the sequence Default button Returns parameters to default values Setting In the Internet BLAST Search Parameterset dialog box clicking the Setting button displays the following dialog box You can specify search conditions when using the NCBI site to perform homology search OM Froeram Obe SSS i J AA Programe bip Database fe Se tion Word size forrucleotide 11 Word site tor protein fB Expect X 10 I Perform urespped slienment Filter I Lom complexity I Haman repeats 7 Mask for lookup table only Mask lower case Description 100 Alignment 100 Query Geretic Codesblastx only Stands Std Sena fa 3 oF enter your organism name here Evetence coat Per residue gap cost 087 1 987 BLOSUNBO 10 1 os BLOSUME2 11 1 O85 default BLOSUMS 14 2 on PARO 7 2 090 zl Output HTL part I Outpt TEXT part Note For details abou
255. lasmid Maps sssssunseununnnunnnnnnnnnnnunnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nna 265 6 2 Create a Plasmid Mapsin sannara ae apea taae Daa aerae ranen jetcetageacedvatneciseters daectesetastngeeded 266 6 3 Map Editing WindOW sssssusssenunrunnnnnunnnnnnunnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn ennnen nna 267 6 L MEU e oe EA EA AER EAEE EE ASE EA OE E VOE NEE AE EEO E E ETO amie 267 603 2 Tool ater scree tities EEE AAEE EEE AEE RUA KEVA EAEE aa A E NA EOR ERNE EAE 268 6 3 3 Status Bat sean nn a A A RTE E A a A R VEE a E T A E T E E ARTENE 269 6 4 Draw in Plasmid Mode ccccccceceseeesssesesneeseeneeseceeeseaesesneeseseeeseaesesaeesnaeeeseseesssesenneeesnnens 270 Addi Restriction Enzymes oi e E di nclennii AE O dis teetensin tata tenuis O ER 270 Inserin e DNA yeee aea E E O EEE A EEE E E EE 271 Adding an Annotations sesser ss ieira onp e e cuss E EE OTE ava EE K EEKEREN T EREKE PESEE REIES TEKEE 272 Change the Plasmid Circle 3 22 cascisi enon aha E N N mane amen 272 Change Restriction Enzyme 273 Change the DNA Change Annotation Length om Delete Ob Cts nis coca achachec sae a dia casasd e A R E EE a ale E tinh denn dada 275 xii Contents Importa File sess iaces menaa oR EERROR E EAEE EARO E 275 6 5 Drawing in Normal Mode sssssssesnuenunnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnunnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnn 277 Add Normal Figures ie nanea a A A
256. lays a list of multiple alignment profiles The following describes the meaning of each column You can click the header of the column to sort the list in ascending order using that column as the key To sort the list in descending order click the column header again Click a profile to select it You can also select a range of profiles by Shift clicking them and select multiple profiles by Ctrl clicking them You can press the F2 key to edit the profile that currently has a focus enclosed by dotted lines Column name Description Name Displays the name of the profile with an icon indicating the profile type The following icons are used a DNA sequence MH Amino acid sequence DNA sequence read only MH Amino acid sequence read only Note Read only profiles cannot be overwritten during analysis with the multiple alignment profile create button of Seqs Displays the number of sequences in the profile Modified Displays the date on which the profile was created Comment Displays comments for the profile if any Button name New Description Creates a new profile Delete Deletes the profile Chapter 5 Button name Databases 251 Description Property Displays the attributes of the profile in a dialog box You can edit some of the attributes Import Imports a profile from a text file created with the export feature Export Exports the selected profile or profile
257. ld_Mitochondrial Kind of Cut_ a O Aar Mycoplasma 7 not identified Shock Selevied 4 Plant Mitochondrial feet Aatl Protozoan Mitochondrial 6 blunt cut Uncheck Selected pcer Vertebrate Mitochondrial H fia Rot h sast Mitochondrial Code TE fee Aaul Useri 6 5 extended SEN Ciis Acc113 User2 6 blunt cut Lis accter Use 6 blunt cut Show Selected Df Acc36l Standard 14 Brextended CE Acces Mold Protozoan Coelenterate Mitechonderial E Pianki Show Checked Le Mycoplasma Spiroplasma OS AccB11 Echinoderm Mitochondrial 6 5 extended CE Acces71 Alternative Yeast 11 3 extended Show Unchecked hm Ascidian_ Mitochondrial Cites AccBSI Flatworm Mitochondrial 6 blunt cut WES AccI Blepharisma 6 5 extended Help Fs Aoc lite Macronuclear and Dasycladacean ANA ee Dlana Dianai i Restriction Enzyme Database Manager Cancel 3 Click the OK button Selecting a Restriction Enzyme 1 Click the Mutation Site Search icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and the Mutation Site Parameter Editor dialog box will appear Codon Table R Output as HTML format Check All Restriction Enzyme List Uncheck All 7 Enzyme Name Recognition Sequence I Bases Kind of Cuta SRA fes BsrSI ACTGGNI NOICAGT 6 S extended ees Dike Bss Al RICCGGY 6 5 extended Uncheck Selected Lite Bss C1 CICNNGG 6 5 extended os BssHI GICGCGC 6 5 extended Show All fies BssKI ICCNGG 5 5 ext
258. lignment display mode it is possible to change the display order About the Target Usually a single sequence is the target of analysis except for two analysis groups the DNA multiple sequence and the amino acid multiple sequence If you click either of those analysis buttons some sequences become the analysis target These sequences called the target have their sequence names underlined The sequence name for the current target also appears on the status bar located at the bottom of the window You can switch the target by clicking the sequence name Selecting Sequences as the Target of Editing Clicking a sequence you want to edit causes the Insertion Pointer to appear there so that you can edit it Selecting Sequences as the Target of Analysis If you left click the name of a sequence to analyze the sequence is set as the target and it is underlined The sequence name for the current target also appears on the status bar located at the bottom of the window Analyzing Multiple Sequences at Once Multiple sequences are required for two types of analysis groups the DNA multiple sequence and the amino acid multiple sequence Therefore the target of analysis covers not only the target sequence but also all the sequences that are currently displayed To remove it from being analyzed hide the current sequence temporarily Usually a single sequence is the target of analysis except for two types of analysis group
259. ll appear before starting the analysis 4 The analysis result will appear below the sequence or in a separate window Tabs classify the Analysis buttons How to Display the Result of Analysis There are two ways of displaying the result of analysis Inline view The result of analysis is displayed below a sequence so that the result is synchronized with the sequence It appears in both the Sequence View and Map View Types of analysis cover the GC content ORF translation and restriction enzyme search Another window The result of analysis is not displayed in the Main window but in another window Results of analysis cover the frequency of codon use and the phylogenic tree SS ame me pome m errre oe erettrno e M eee ssf S84 880 enpa gt gt r naagador f i zem Oe gt Inline Window Another Window The type of analysis automatically decides whether display will be in a new window or inline Customizing the Display of Analysis Results Refer to Chapter 3 Details of You can customize the display of results of analysis for example changing the color and hiding some of the results Analysis Right click the results of analysis to display the menu where you can perform operations For details refer to the description of individual analysis results 34 DNASIS Basics Changing Analysis Parameters Some items of analysis require paramet
260. log box will appear Click the Parameter button and BLAST Parameters will appear Blast Parameters Program name x Detail Expectation value 10 v Default IV Filter query sequence Descriptions 100 fw IV Include gap in alignment Alignments 100 X Amino Acid Database PIR __ Select All Deselect All __ Setting Help OK Cancel 2 The Amino Acid Database field lists the databases Place a checkmark in the check box for the target database 3 Click the OK button 156 Details of Analysis 3 37 Internet BLAST Search Amino Acid Types of BLAST Search There are three ways of BLAST search for amino acid sequences Button name Program name BLAST search blastp Description Performs homology search between amino acid sequences and an amino acid database BLAST search tblastn Performs homology search between amino acid sequences and an amino acid database Translation DB translated in all frames One to One blastp Performs a homology search between two different amino acids BLAST Search Explanation of the Result Window Refer to the Explanation of the Result Window in Section 19 BLAST Search Selecting a Database to Be Searched excluding one to one BLAST search 1 Click the BLAST Search button from analysis button view and an Analysis dialog box will appear Then click the Parameter button 2 Click the Setting button to display the NCBI Advanced BLAST Search window
261. lygons The same as Object Normal gt Polygon in the menu Creates text areas The same as Object Normal gt Text in the menu Creates balloon texts The same as Command gt Label in the menu Draws spirals of Spiral Type alpha helix The same as Object Normal gt Spiral Type alpha in the menu Draws spirals of Spiral Type beta helix The same as Object Normal gt Spiral Type beta in the menu Adds restriction enzymes The same as Object Plasmid gt Add restriction enzyme in the menu Adds DNA to the positions of the selected restriction enzymes The same as Object Plasmid gt Insert DNA by enzyme in the menu Adds annotations to plasmid regions The same as Object Plasmid gt Annotation in the menu A OE aA QF YO 7 2 5 BB S Deletes selected restriction enzymes DNA or annotations The same as Object Plasmid gt Delete Object in the menu Chapter 6 Create Plasmid Maps 269 Icon Description ct Reads in external files The same as Object Plasmid gt Read file in the menu Auto align or not control The same as Alignment of Label in the menu 6 3 3 Status Bar Normal Figure Displays the current edit mode Normal or Plasmid 270 Create Plasmid Maps 6 4 Draw in Plasmid Mode In Plasmid Mode plasmid maps can be drawn and edited To create or edit in Plasmid Mode select Command gt Plasmid Figure in the menu or click a on the Toolbar When drawing in
262. m2 mRNA complete cds U33203 992684 human Homo sapiens Eukaryotae mitochondrial eukaryotes Metazoa Chordata Vertebrata Eutheria Primates Catarrhini Hominidae Homo 1 sites Sigalas I and Lunec J Multiple alternate spliced mdm2 transcripts with loss of p53 binding domain sequences transforming ability and frequent detection in human cancer Unpublished 2 bases 1 to 309 Lunec J Direct Submission Submitted 04 AUG 1995 John Lunec Cancer Research Unit University of Newcastle Upon Tyne Medical School Framlington Place Newcastle Upon Tyne NE2 4HH U K Location Qualifiers 1 309 organism Homo sapiens db_xref taxon 9606 map 12q sex female tissue_type primary ovarian tumor chromosome 12 1 309 238 Databases gene mdm2 CDS 1 309 gene mdm2 note mdm2 alternatively spliced form e codon_start 1 evidence experimental product mdm2 E db_xref PID g992685 translation MCNTNMSVPTDGAVTTSQIPASEQETLVRPK PLLLKLLKSVGAQKDTY TMKEVLFYLGQYIMTKRLYD EK QQHIVNDCANLFPLVDLSIRELYISNYITLGI BASE COUNT 100 a 57 c 53 g 99 t ORIGIN 1 61 121 181 241 301 atgtgcaata ccaacatgtc tgtacctact gatggtgctg taaccacctc acagattcca gcttcggaac aagagaccct gettagacca aagccattgc ttttgaagtt attaaagtct gtteggtgcac aaaaagacac ttatactatg aaagaggttc ttttttatct tggccagtat attatgacta aacgattata tgatgagaag caacaacata ttgtaaatga ttgtgctaac ttatttcccc tagttgacct
263. me window appears Delete button Deletes the selected restriction enzyme from the database To delete more than one enzyme select the enzymes you want to delete and then click this button Property button Allows you to edit the restriction enzyme The Enzyme Property window appears Import button Imports restriction enzyme data from an external file Export button Exports restriction enzyme data to an external file Help button Displays online help OK button OK button Exits from the Restriction Enzyme Database Manager New Enzyme window You can use this window to create a new restriction enzyme Enzyme Name Restriction Site ____ Normal Complementary The number of bases 0 Kind of Gut Details follow Item parameter Enzyme Name text area Description A text area used to enter the name of the restriction enzyme you want to create The OK button is disabled if this area is blank Normal text area A text area used to enter the recognition sequence for the restriction enzyme you want to create Enter the recognition sequence using a complex code containing characters from the string ACGTURY WSKMBDHVN not case sensitive Enter an exclamation mark at the position to cut Specify the characters in the direction from 5 to 3 Complementary text area A text area used to enter a complement recognition sequence if the restriction enzym
264. mentarity Specifies the maximum allowable value for an alignment score when 3 end alignment is applied to a single primer or between the left and right primers You can use this value to predict the trend in primer dimer forming for PCR A score is calculated in the same way as with Max Self Complementarity Max N s Specifies the maximum of number of Ns undefined bases that can be allowed for the designed primer Max Poly X Specifies the maximum number of consecutive identical bases e g AAAAA Inside Target Penalty Currently not supported Outside Target Penalty Currently not supported First Base Index Enter 1 for DNASIS GC Clamp Designs a primer having a specified number of consecutive GCs at the 3 end of the left and right primers Salt Concentration Specifies the salt generally KCl concentration mM for PCR Used to calculate a Tm value Annealing Oligo Concentration Specifies the annealing oligo concentration nM for PCR Used to calculate a Tm value Liberal Base Selecting this check box enables DNASIS to accept a complex code an asterisk and a hyphen by replacing them with Ns Pre Sequence Inputs PrimerParameterEditor x Penaky Weights for Primes Genel Parameters Hyb Oligo Conditions Penaky Weights for Hyb Oigo Primet Picking Conditions Pre Sequence Inputs Included Region Start Codon Position Sequence Quality Zi Min Sequence
265. n 3 Select the parameter then click OK List up Search Results Select the Common Motif Sequence right click and select the Show Common Motif Dialog or for a frame in sequence view select the sequence name and analysis name then click the Result List Dialog button and the search result list will appear Common Motif Dialog Eile Edit Help E 5 gt OB alal ASN_GLYCOSYLATION lol x O maS S EE E E r M CK2_PHOSPHO_SITE PROSITE Release 13 PROSITE Release 13 7 HYRISTYL PROSITE Release 13 M PKC_PHOSPHO_SITE PROSITE Release 13 TA AMTDATION PROSITE Release 13 M CAMP_PHOSPHO_SITE PROSITE Release 13 M CYTOCHROME C PROSITE Release 13 Chapter 3 Details of Analysis 151 Use Copy All or Copy Selected from Edit in the menu to copy all or selected cells to the clipboard as tab delimited text Use Save All as or Save Selected as from File in the menu to store all or selected cells in a file as tab delimited text Browsing Annotations of Searched Common Motifs Click D from the Common Motif dialog to display a motif annotation tif Annotation Dialog Motif Name CARS Motif Pattern OF EDRKHPFYWIEHSTAGONIL P Motif Annotation APENE PATTERN APR 1990 CREATED APR 1990 DATA UPDATE APR 1990 INFC N myristoylation site G EDRKHPFYW x 2 STAGCN P TAXO RANGE 7E SITE 1 myristyl SKIP FLAG TRUES PDOCO00008
266. n 1 bp M Nmf Z 2 Click the Parameter button from the Analysis dialog that appears Genelndex Homology Search Comment Conduct Homology Search in Genelndex Launch parameter editor to change species J7 Execute analysis without showing this dialog gt t Parameter Execute Close 3 A settings dialog will pop up where you can enter GeneIndex login information Enter the appropriate information When you start up for the first time no species is registered in the species list combobox After entering the 168 Details of Analysis appropriate value click the Update button and it will then be possible to access the GeneIndex server to obtain a species list d GenelndexParamEditor i x Genelndex Server ONASIS Pro Account Leen D am DNASIS Account Password pme o Genelndex Contract Account Contract ID AAD Genelndex Account Password pem Select Soecies Species 4 And click OK Homology Search Use amino acid sequences and DNA sequences to perform a GeneIndex Homology Search When using this search a sequence that displays in DNASIS MAX will appear in the search string of the GeneIndex Homology Search It is possible to specify other conditions then perform the search Select Target Sequences The sequences that display in Sequence View are the target in the Homology Search You will have to hide sequences you want to remove from the search target 1 Enter a new se
267. n Enter or paste a motif you want to search for IV Use Input Pattern MWA TOW Help Cancel 3 Click the OK button The Analysis Result View shows a motif that has the name Input Pattern Displaying a List of Search Results For the frame in sequence view select the sequence name and analysis name then click the Result List Dialog button Nucleic Acid Motif List 0 x File Edit Help BS gt alal WotifName _WotifPattern_ Start bp End bp AARKGA lv jalpha_INF 2 1355 1360 Norma M 1870 1875 Normal v 2643 2648 Normal v 2776 2781 Normal M AP_1_CS3 TGANTHA 2191 2197 Normal v 2486 2492 Normal ical 2434 2500 Normal Vv 2594 2600 Normal M AP_2_CS3 COSCRGGC 186 193 Normal v 426 433 Normal Voo erir 668 675 Normal M AP_2_CS4 YCSCCMNSSS 176 185 Normal vw 177 186 Normal v 178 187 Normal v 182 191 Normal v 665 674 Normal M AP_2_CS6 CCCNNSSS 152 159 Norma K 153 160 Norma T ical 165 172 Normal iv TH 184 Normal v 178 165 Norma v 173 186 Norma v l 180 18 Normal iv 604 611 Normal M 668 675 Normal Iv 365 972 Normal v 1104 1111 Normal xl 7 ARC DRI T Cancel Z Use Copy All or Copy Selected from Edit in the menu to copy all or selected cells to the clipboard as tab delimited text Use Save All as or Save Selected as from File in the menu to store all o
268. n Enzyme Database cccccsccecsssnneeeceneeeeseeeeeeeseeeeeeeseseeeeeseeeeeeessseeeeeeeseeneeeeseenens 243 Window Descripttottss s oeeie irei eE aerieni rE Er a uaeacesncbsedetasadagedacvaedetavavacestevadersevanntetacuneeiees 243 Parameter Description cccesesesseeeeeeees 243 Example of Registering a Restriction Enzyme 245 Enzyme Property Window cceseeeereees we 245 Importing Restriction Enzyme Data vrs iscescensesccxesvenceeesaanecusananccecsnanceneasavecersesncdhsna rcunesnsatcevsbancuteynanteces 246 Registering a New Restriction Enzyme ccccccecceseesseseeseceeceseeseeseesececeeeeaeeaeeseeseceeeeaeesecaeeeseeseaeeaeeaeens 247 Exporting a Restriction ENZYME oi cisicssissssstsscesscedsscesscasccessadaatesscasccessad acca sacsseceveedaseasscstavessedaseasssanavevecaaes 248 Complex Code ees nessa ce ne ass el cas cds eee EES 248 Restriction Enzyme Data Format jccccavsaxccsseveasecetssaucissscececevevavesavedececunsvavsiavedeicevalekosievedeteeseseastesveeatedes 249 5 7 Multiple Alignment Profile cccccessseeeeeeeeneeeneeeeeeeneeeeeeeeseeeeeenseceeeeesseneesaaseeeeeesseeeeeeeseeenens 250 Multiple alignment profile ives cod ssedsscssiss scot sees tessere bron oirr iaeoa Eeid op Ee Sr SEESE E SIS SEES o PEIEE EEs 250 Window Description ys caeno ii n E ea EEA E ORAE R O T E a O Avi madden Aeimaident 250 Property Wii OW EE EAS NEEE EAEE AASE ETS S LA EEN EE E EEE E E 251 5 8 COGOMN Table ii scciccaiscs
269. n anc e suerte ested diateearsaseddeea sas teeter se eet aa 73 Changing Codon Tables ois iit a ee ce ee ee dE A KEERAS 73 Changing the Display Color of Amino Acids eeceecceeseescseeseeeeseeeeseesesecacecseeaeseeseeesaeeecsesaseesseeaeaees 73 Editing and Analyzing the Result of Translation ccccssscesseeseeseeseeseesecseeeececeeeeseesececeeeeseeaeeaeeaeeneeenes 74 3 0 BASE CONteNt visiei sscccensuvedaunessitevnswebassievasnscsawasdsuuiensdlgunacsedsund su anleunavesisaidandnenvagetevebdsauseetaeuavansss 75 Explanation of the Result Window c ccssscssseseeseceseeeceseeseesecsecsecseceseeseeaecseceeeeseeaecaecaecaeeeeeeeeaeeaeeneeaees qd 3 7 Codon Usage ecccceseereeeeeees Explanation of the Result Window BI Chan ping the Brame 22 5522 e eea E ERE RR RE EEA AE AEEA ANE ENES EEEE E LRN GC OTe i TaI AEA E A T E E scutvenceons Explanation of the Result WIndows cisve cus ens erne ae R E R ERO E R E Customizing the Result Displays mennaan e Ee A A AEA A 3 9 Vector and Low Quality End Trimming cccsecceseceeeeeeeeneeeeeneeseeeseseeeeeeeeeseensesnaeeneeeeesenes 80 Contents vii Explanation of ithe Result Window ccccsvsneccsssesntaststoaease soncesestvnezsdesuelacdsbvauzedeseades saueuzedestaedsstauauesiessadeceeey 80 Trimming Only Vectors sic ssiveay tee aeaa Ea eee a acacia cee Pannen ees 80 Registering New Vectors onirin ne E E RRE E E E E E AN set 81 Trimming Low Quality End s
270. n double byte characters and these characters that are not supported for file names 2 lt gt DB Lock Indicates the lock state of the motif database Place a checkmark in this box to lock the database to prevent it from being edited of Motifs Displays the number of motifs stored in the database Last Modified Date Displays the date when the database was edited last Comment Displays comments for the database ifany You can edit the comments if the database is not locked OK button Saves the changes made to the properties and closes the Nucleic Acid Motif Database Property dialog box The changes are canceled if a database having the same name is already registered Cancel button Discards the changes made to the properties and closes the Nucleic Acid Motif Database Property dialog box Displaying a List of Registered DNA Motifs You can display a list of all motifs registered in the DNA motif database In the Nucleic Acid Database Manager select the database for which you want to list the contents and click the View button Item Nucleic Acid Motif Database Database Name SAMPLE Name Pattern Annotation 28S_RNA_termination AGGTCGACCAGW 1 GTGNNGYAANNNN AABS_CS AABS_CS2 GTGNNGYAA ABF1_CS WDCNYNNNNNAC GNGCCGNCGCCG ae GNGTCGNCGTCGN Alb_PE ARTTATTGGTTRG alphal alpha2_el AARKGA TAATGARAT AWWTATNCAT STGACTMA TGANTMA TGASTMA TCCCCANGCG COGCCAGGG
271. n on the toolbar Display in 2 9 Editing and 3 A sequence whose name begins with Untitled001 is added to the end of the sequence list Analyzing 4 At the Insertion Pointer which is flashing at the start of the sequence enter an appropriate sequence from the Multiple keyboard as shown in the figure Sequences rorererererarara AF165046 Sequence Untitled001 Sequence POPEO r AF165046 Sequence aagcgtctag ccatggcgtt agtatgagtg AF165046 Sequence 190 assssssasl ssis AF165046 Sequence ctttcttgga tcaacccect caatgccteg Creating a New Sequence from Part of an Existing Sequence You can extract any range of any sequence so it can serve as another sequence 1 Select any range of any sequence as shown in the figure Sequence 10 20 30 40 AF165046 Sequence ttgggggcec cactccacca tagaccactc cectgtgage aactact 70 80 90 10 AF165046 Sequence aagcetctag ccatggcgtt agtatgagts testecagce tecaget 130 140 150 160 AF165046 Sequence gagagccata eteetctece gaacceetea etacaccega attecca 190 200 210 220 AF165046 Sequence etttcttega teaacccect Caateccteg agatttgzgc g gcccc 250 260 270 280 AF165046 Sequence gcceagtagt ettegetcoec gaaagecctt etggtactec cteatag 2 Select Sequence and then New DNA or click the oe button on the toolbar 3 A sequence whose name begins with Untitled001 is added to the end of the sequence list The sequence corresponding to the range selected in ste
272. naees 216 428 AMINO Acid CON eN rr a aaa E rar raaa aea raar aa aa aA aar a aE a heoa aaraa Aadan na HA Enar eais 218 4 29 Is eletric POINnt iiccccseiceeieescceccceedctetessteedenetctedeenccecceendctedeesscecdessdccnived NEANS EAH KARENE NENANA KAE 219 4 30 Hydrophilicity Hydrophobicity and Secondary Structure cccccceesseeeeeseeeeeeeeereeees 220 4 31 Proteolytic Site Search cceeesceceeseneeeeeeeeeeeeeneeeeeeseeeeeeeseneeeeseeeeeeeseeeeesseeeeeeeaseeeeeesseeneeenss 221 A S2 ANMOtAatlO e eeraa e coves a a ae dul eccceginvecavesctdBueeceedeestes duceahereacese ccedesecuvdenstucceueceeetevesd 222 Chapter 5 Databases ssessssuunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnmn nnnnnn nnmnnn nenna 225 5 1 List of Databases ai ieccs ceccciccccticiceievedessttieete ininda anniina aaki araia redeed teat tecies eededescatetee te eeteeeid 226 5 2 Sequence Database nni aea aana ea aa aana na Eaa eaaa eaea aaae aitaan daami 227 Creating a New Database scsssssscssssssssssscssssssssssccesssstsseseccesssnisseecesssnsseseesssnussecesssnssesensnnmesseeeee 227 5 3 Registering an In House Database cccccsseecceeseeeeeeeeeeneeseeneeseeeeeeseeeseeeseseseaeseeeseanseeeenes 230 Selecting a Destination Database csssssssssssssssssesssccessssseessccessssseesecessssussesecessssnsseceessnnieseceessnnneesss Registering a Sequence in the Database Creating an In house Database cssssssssssssssssssssesccsssssseescesssssnnsesec
273. nalysis are the same as 4 10 Primer Design describes 192 Details of Parameters 4 12 Restriction Enzyme Site Search Restriction Enzyme List Show All Enzyme Name Kind of Cut__ AE Aar CACCTGCNNNNINNNN NNNNNNNNGCAGGTG 15 5 extended aneii es AasI GACNNNNINNGTC 12 3 extended ce Show Checked Ds Aatl AGGICCT 6 blunt cut zs Aat GACGTIG 6 9 extended Show Unchecked aes Aaul TIGTACA 6 Stextended fest Acc 131 AGTIACT 6 blunt cut Ta AEE Acct 61 TaCIaca 6 blunt cut Check All DOE Acc36l ACCTGCNNNN NNNN NNNNNNNNGCAGGT 14 S extended O Acc6sI GIGTACC 6 5 extended raresa i AccBII GIGYRCG 6 Shextended DOE AccB7I CCANNNNINTGG 11 3 extended AS AccBSI COGICTC Gaaicaa 6 blunt cut Ta Dis Accl GTIMKAG 6 5 extended O AccI calca 4 blunt cut Es Acci TICCGGA 6 5 extended z ARE Acelll CAGCTONNNNNNN NNNNANNNNNNNNNNNGAGC 17 S extended 4 eee Acil CICGC GICGG 5 extended ha 4 OK Restriction Enzyme Database Manager Cancel Item Description Enzyme Name NAME Shows the name of restriction enzymes Using the restriction enzyme with a check in the leftmost check box the cut region will be analyzed Recognition Indicates the sequence that a restriction enzyme recognizes in the Sequence SITE_N SITE_C direction from 5 to 3 The part indicates the place to cut When the recognized sequence is not in a palindrome structure the sequence that the Normal strand recognizes and the sequence that Complementary stran
274. naseneens 105 Displaying a List OF Search RESUS moare E a EE R E EAEE 105 Settitig Parameters scx EE E TA E E AAO ON OR 105 3 18 Tandem Repeat Search c isinin tee kaanane einasi aaa aaa aana ha manana an na ahaaa naa aaea Anaia 107 Explanation of the Result Window Displaying a List of Search Results 107 Annak Parameters cca estes chen EE TEA TE E E E ON eRe 107 3519 BEAST SOOM oce E E E a E s 109 Typesof BLAST Search ccdi cis aoo i e AE RR A E ERRER EERE E AREK R R ER E 109 Explan tion ofthe Result Window ssvecsevevcssevse ccvevectcse cies taseescaease sees etcss A NEE A EA EAE 109 viii Contents Selecting a Database to Be Searched other than one to one BLAST Search ssssssssssssssseseseersrsreresee 111 Obtaining an Entry to the Result of Search ansionsa oiii iiaae EA NEE NE 112 3 20 Internet BLAST Search c ccc ccceescce essen sesneseneesssneesesneessesusneesasneeeseneessaesesneesaaneueesnenas 113 Types of BLAST Search 113 Explanation of the Result Window 113 Selecting a Database to Be Searched 113 Selecting the Species zs 5 cs5e5 cieesbs Ssncsstsesecssbesacssibdsde saeeseetsiasdesestesastactdsestuessasvnles seevstbesacsidnasdovsaaneseveinesy 113 3 21 Smith Waterman Search ccccccsccc ssc eeeeeeseceeesceesesneeseeneeseceeesceesesneeseseeeeceeasssaesseneesennenss 115 Types of Smith Waterman Search s5 Explanation of the Result Window cccescsssess
275. nce database One to One Performs a Smith Waterman search between two different DNA sequences Smith Waterman Search Explanation of the Result Window Refer to 3 19 BLAST Search Selecting a Database to Be Searched Smith Waterman search only 1 Click the Smith Waterman Search icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a GENE BRIGHT III Parameterset Editor will appear Caloulate by Bottware Emisio r T hps Sequence Type DNA Matr DNA hetal Gap 5 al Extention Gap 4 Max Nan ot Return i F Cut Off Score Tareet Database Exsrpie Select All ee HSK blsstn2seq J HSK SW2eeg NA Develect Ae House NA jw man 2 In the Target Database field place a checkmark for the database to be searched 3 Click the OK button 116 Details of Analysis 3 22 Multiple Alignment This function calculates and displays a multiple alignment of all sequences displayed in the window ie Sequences in a project using the Clustal W algorithm Explanation of the Result Window aittxi ie oa omo Yew feb oe Bega ad is ae S265 22427 vs em Dah wias Map View iz Sequence View 5 Map View This view displays matching conditions in the entire alignment If you move the cursor the Map View also moves accordingly Sequence View This view displays the alignment according to the perfect match partial matc
276. neIndex 2 2 Operation Manual Chapter 4 Details of Parameters 173 Chapter 4 Details of Parameters 174 Details of Parameters 4 1 Complement Sequence No parameters Chapter 4 Details of Parameters 175 4 2 Reverse Complement Sequence No parameters 176 Details of Parameters 4 3 Reverse Sequence No parameters Chapter 4 4 4 Translation Codon Table Universal J omei Item Description Codon Table Selects a codon table used for translation Details of Parameters 177 178 Details of Parameters 4 5 Base Content No parameters Chapter 4 Details of Parameters 179 4 6 Codon Usage Codon Usage Start Position M ome Item Description Start Position Specifies the base from which DNASIS starts counting codons You can specify First Second or Third 180 Details of Parameters 4 7 GC Content Window Size oare Item Description Window Size Specifies the sequence window size for calculating the GC content Chapter 4 Details of Parameters 181 4 8 Vector and Low Quality End Trimming E Trim End F 5 Exo I Trin at bast m I Trim the first 10 tp while the quality is bees thar D g F F ENO Ja vam Hon E W Same az amp END F Trim vector select your cloning site tf you pant to choose double cloning she select with Girl Key Window size for vector Yirening 20 t Minimum Matching Percentag
277. nite Piles 4 Once dropped the file is read and the corresponding sequences are added in the window in 2 3 Using Existing Files 5 It is also possible to select multiple files and read them at once Readable File Formats The following is a list of file formats that can be read and displayed in DNASIS These formats are automatically identified by DNASIS according to the contents of files You do not need to be concerned about the extensions of file names because they will be ignored Chapter 2 Refer to 2 11 Annotations DNASIS Basics 25 Format DNA Amino acid Annotation Trace data sequences sequences RD Readable ME It is possible to read multiple entries from a single file NR Not readable NA No applicable data Annotations can be read in the Comment View For details refer to Comment View in 1 2 Description of Individual Parts By analyzing the Features or function descriptions as part of sequences it is possible to display and edit them in the form of annotations For details refer to 2 11 Annotations For EMBL format files it is possible to show and edit annotations in only EMBL Nucleotide Sequence Database For details about annotations refer to 2 11 Annotations You can display and edit trace data after reading it For details refer to 2 14 Waveform Display Mode Reading Files in the FASTA Format In this format the entry begins with gt The part ranging
278. nment of Label Selected When editing the restriction enzyme is automatically realigned Not selected When editing the restriction enzyme position does not change Help menu Description Version Displays version information 6 3 2 Toolbar e 2 lees oSA les Icon Description Closes the Map Editing window The same as Command gt Exit in the menu at For inputting and editing normal figures Normal Mode The same as Command gt Normal Figure in the menu x For inputting and editing plasmid figures Plasmid Mode The same as Command gt Plasmid Figure in the menu Cuts the selected object The same as Edit gt Cut in the menu Copies the selected object The same as Edit gt Copy in the menu Pastes the cut or copied object The same function as Edit gt Paste in the menu Cancels the previous operation The same as Edit gt Undo in the menu Restores the canceled operation The same as Edit gt Redo in the menu Displays the properties of the selected object The same as Edit gt Properties in the menu Draws straight lines The same as Object Normal gt Line in the menu Draws arrows The same as Object Normal gt Arrow in the menu Draws curved lines The same as Object Normal gt Curve in the menu Draws rectangles The same as Object Normal gt Rectangle in the menu Draws ellipses The same as Object Normal gt Ellipse in the menu Draws po
279. nnn nennen 195 4 15 Haripin Loop Searchissa svete neue inana akn adaa anadan ite iaaiiai 196 4 16 Stacking Site Search sec cicccccecisececeesscccntessececs ex steneesuecenceessendaesezecneeexscuntesisecnetevsccaere iecger exe 197 4 17 Tandem Repeat S archi isi naana a aeara arrama Ean Eaa ahe a ai ankenia E aaki Naai aauina 198 4 18 BLAST Search DNA and Amino Acid ssssessseeneneunnnnnnnnnnnunnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnna 199 4 19 Internet BLAST Search DNA and Amino Acid ccceeeseeeceseeneeeeeeeeeeeseeneeeeseeneeenseeneeenes 200 4 20 Smith Waterman Search DNA and Amino Acid cccceeceeeeeneeeeeeeeeeeeeeeeeeeeeeeeeeeneeeneeenes 201 4 21 Multiple Alignment DNA and Amino ACiQ cccecesteceseeneeeseeneeeeeeeeeeeeseeneeeeseeneeeeneenenenss 202 4 22 Phylogenic Tree DNA and Amino Acid ccccccceeeeneeeeeeeneeeeeeeneeeeeeceeeeeseeeeesaseeneeenseeneeenss 207 4 23 Creating Multiple Alignment Profiles DNA and Amino ACiQ cccsssseeeessereeeeesereeees 208 4 24 Phylogenic Tree Using Profiles DNA and Amino Acid cccsssseeeesseneeeeesereeeneeeteeenes 213 A 25 SCQUENCE ASSEMDIE e niece a a a r aaaea A a a a a a Aaaa aa Aaaa rie ae couvaniecebey etessnasen 214 4 26 Clustering 02 ccciiecdcccccesdacediesteecctend dectiendebeceesd detctesdececdend NEENA NAAR EN Ep AA RENE EPEN AKARAN CNAS 215 4 27 BLAST Search and Extraction ccccceceeeeeeeeeceeeeeeeeeeeaneeceeeensnesseeeeeseeesnaenseeeeeseeee
280. not specified It is also disabled if the Motif Pattern Test Sequence contains anything other than alphabetic characters lt button If more than one section matches as a result of a pattern test clicking this button highlights the match previous to the one currently highlighted This button is disabled if the first match is currently highlighted gt button If more than one section matches as a result of a pattern test clicking this button highlights the match following the one currently highlighted This button is disabled if the last match is currently highlighted Motif Annotation Annotation of the motif You cannot edit this item if the database is locked Help button Displays online help OK button If you have opened the dialog box from the Property button the OK button saves the changes made to the motif data and closes the dialog box If you have opened the dialog box from the New button the OK button adds the motif data and closes the dialog box You cannot register a motif having the same name as that of an existing motif You cannot register a motif if its motif pattern is invalid This button is disabled if the database is locked Cancel button Discards all changes and closes the dialog box Chapter 5 Databases 257 5 10 Proteolytic Enzyme Database DNASIS MAX supports the functions for creating editing deleting importing and exporting proteolytic enzyme data Window Descri
281. notation from Edit in the menu xine Ole lO The same as Copy Selected from Edit in the menu gc The same as Check All from Edit in the menu ALL cy The same as Check Selected from Edit in the menu ack The same as Uncheck All from Edit in the menu The same as Uncheck Selected from Edit in the menu Chapter 5 Databases 225 Chapter 5 Databases 226 Databases 5 1 List of Databases The following table lists the databases that DNASIS provides These databases are listed under Database in the analysis tools menu For details about each database see the page shown in the Page column Sequence database In house database registration DNA sequence In house database registration amino acid sequence Vector database Amino acid motif database Restriction enzyme database Multiple alignment profile Codon table DNA motif database Proteolytic enzyme database BLAST search dedicated database Chapter 5 Databases 227 5 2 Sequence Database The Sequence Database Manager lets you manage sequence databases For example it lets you create delete or browse a sequence database You can use a sequence database to create a database for BLAST searches or Smith Waterman searches SSH In House AA 2001 10 11 Ih House NA 9 nfl dois P MAM 33540 2001 8 19 other mammalian sequences WH PIR 239 764 2001 8 31 This database is derived from the PIR
282. ns Then click the Parameter button Chapter 3 Details of Analysis 127 5 zj General PainmisAerrent MultipleAlierenent ProteinGsp Tree Profile Mame ST NA Sequence Type paa Quiot Order Order by Alipred w Protile WNansger I Lee FAST Aleorithen tor the alanmert Protein Chars ABCOEFGHIKLNNFORSTUVWYZ DNA Chars ABCOGHENRIRSTUVWY Cox ee e 3 In the Profile Name field select a profile you want to create and click the OK button or to create a new profile select Profile Manager 4 Click the Create Multiple Alignment Profile button DNASIS uses all sequences displayed in the Sequence View to perform multiple alignment and then writes the result into the profile Note Note if you had chosen an existing profile name the profile is overwritten Locking the profile prevents an Refer to 5 7 Multiple Alignment Profile unexpected overwrite Use the Profile Manager for locking the profile Using a Created Profile on Another PC You can export a newly created profile and save it to a file You can also import such an exported profile to use it on another PC Export Procedure 1 Click the Create Multiple Alignment Profile analysis menu and an Analysis dialog box Then click the Parameter button 2 Click the Profile Manager button to display the Multiple Alignment Profile Manager window 3 From the display select a profile you want to export 4 Click the Export button The
283. nslate SXxxV al rg XxxGly ORF Move Up Hide Analysis 2 Right click the analysis name 3 When a menu appears select Delete Analysis Hiding the Result of Analysis You can hide the result of analysis temporarily 1 Left click the analysis name for a result of analysis you want to delete Once you left click to select it the analysis name is underlined as shown in figure Chapter 2 Refer to Redisplaying the Result of Analysis in 2 5 Analyzing Sequences basic Refer to 1 7 Data List Window DNASIS Basics CoN Delete Analysis 2 Right click the analysis name 3 When a menu appears select Hide Analysis This redisplays the hidden result of analysis Redisplaying the Result of Analysis 35 You can redisplay a hidden result of analysis 1 Click the E button on the View Toolbar alternatively you can click View and then Data List 2 The data list dialog box appears 3 Select the check box for a result of analysis you want to redisplay so that a checkmark is placed in the box 4 Press the OK button to close the dialog box 36 DNASIS Basics 2 6 Customizing Display of Sequences The number of characters per line to display for sequences or the results of analysis can be selected from three choices No folding back characters folding back characters according to the window width and folding back characters according to a specified
284. nzyme dialog box appears as shown below Enter necessary information and click OK 248 Databases For details about the format of the output restriction enzyme data refer to Restriction Enzyme Data Format in 5 6 Restriction Enzyme Database Enzyme Name r Restriction Site Normal Complementary The number of bases 0 Kind of Cut Not Identified Z Ok Cancel Exporting a Restriction Enzyme You can export a selected restriction enzyme using the Restriction Enzyme Database Manager window Export file dialog box In the Restriction Enzyme Database Manager window clicking the Export button causes the following window to appear us Saven I My Occxevert d Doan iy Pauses y Fae pare Ferrar nare arnese f Seve Seve arte Aemet Ename Hes l erepre Cocea Specify the destination folder and file name and click the Save button DNASIS outputs the data of the restriction enzyme that was selected when you clicked the Export button Export errors The following two errors may occur during export 1 Enzyme Name has too long name You can t export this enzyme The name of the restriction enzyme Enzyme Name is too long DNASIS cannot export a restriction enzyme which contains this error Correct the name of the restriction enzyme so that it does not exceed 255 characters and reexport it 2 You can t export no name enzyme The restriction enzyme being exported does n
285. o when selecting restriction enzymes from the list it is possible to designate the upper and lower limits of cut frequency Select Enzyme Restriction Enzyme List Show All Enzyme Name Recognition Sequence Kind of Cut a aes Aaul O Acct 131 Ae Acct 61 DMS Acc36l O Acc65I ARS AccBII DOE AccB71 AE AccBSI CACCTGCNNNN INNNN A NNNNNNNNGCAGGTG GACNNNN INNGTC AGGICCT GACGTIC TIGTACA AGTIACT TGCIGCA ACCTGCNNNN NNNN NNNNNNNNGCAGGT GIGTACC GIGYRCG CCANNNNINTGG COGICTC GAGICGG S extended S extended blunt cut 6 3 extended 5 extended blunt cut blunt cut 5 extended 5 extended 5 extended 3 extended blunt cut Show Selected Show Checked Show Unchecked Check All Uncheck All 5 extended blunt cut 5 extended 5 extended 5 extended GTMKAC CGCG TOCGGA CAGCTONNNNNNNINNNNANNNNNNNNNNNGAGC CICGC GICGG DOSS Acct Ds Accll LASS Acci Las Acel ee Acil Restriction Enzyme Database Manager 3 The ones with a check in the box to the left of the Enzyme Name are the selected restriction enzymes Select the restriction enzyme to search and click OK 4 Click OK on the RestrictionSiteParamEditor window Registering a New Restriction Enzyme 1 Click the Restriction Enzyme Site Search icon from analysis button view The Analysis dialog box will appear then click the Parameter button to display the Restriction Site ParamEditor window 2 Select the Select from
286. o Acid Adds an amino acid sequence Duplicate Creates a new sequence by duplicating a currently selected sequence Revert Returns to the pre edit sequence Find Searches for a sequence Find Again Searches for the next occurrence It will become possible to select this only after Find is executed Jump Moves the cursor to a specified position Complement Converts into a complement sequence Reverse Converts into a reverse sequence Reverse Complement Converts into a reverse complement sequence Chapter 1 For details refer to 1 5 Preferences Dialog Box For details refer to 1 6 Internet Setting Dialog Box Window Descriptions 9 Upper Case Converts the expression of a sequence into uppercase characters Lower Case Converts the expression of a sequence into lowercase characters Exchange Case Converts the expression of a sequence with uppercase and lowercase characters Mask Masks the sequence of a range Make Consensus Uses the Editor to enter a consensus sequence as a new sequence in the alignment mode View menu Analysis Button View Function description Views hides the Analysis Button View Comment View Views hides the Comment View Map View Views hides the Map View Data List Displays the Data List window Standard Toolbar Views hides the Standard toolbar Switch Pane Toolbar Views hides the Window Switchover toolbar
287. o search for 3 Click the OK button Registering a New Proteolytic Enzyme 1 Click the Proteolytic Recognition Site Search icon from analysis button view and an Analysis dialog box will appear 154 Details of Analysis Proteolytic Enzyme List Check All Name Recognition Seq Comment Uncheck All Acrosin IKRIX Acrosin O CathepsinB1 RX CathepsinB1 O CathepsinG LYFIX CathepsinG E Chymosin FIM Chymosin O Chymotrypsina FYWIX Chymotrypsina Dchymotrypsinc FYLIX Chymotrypsino 7 O Ciostripain RX Clostripain Show Checked O Cocoonase KR X Cocoonase O CyanoeenBromide MX CyanogenBromide Show Unchecked Elastase AX Elastase Enteropeptidase DDDDKI Enteropeptidase BFicin RX Ficin Ok Cancel Usable Characters Setting Help 2 Click the Proteolytic Enzyme Database Manager button at the bottom of the window 3 Click New on the Proteolytic Enzyme Database Manager window to display the New Database dialog box 4 Enter the enzyme name you want to register the sequence and the comment optional and then click the OK button Displaying a List of Split Areas by Proteolytic Enzymes From analysis result in sequence view select the sequence name and analysis name then click the Result List Dialog button The list of split areas appears You can copy and save any data in the window 5 x File Edit 7 lelp B amp gt alal M CyanogenBromide WIK M Chymot rypsind FWY
288. olling 3 Select Copy and then Copy Image or click the W button on the tool bar 4 Switch to another application such as MS Word and paste the copy Note Copy pasting requires you to specify the following options Paste after Selecting Format Graphics Extended Metafile 64 DNASIS Basics 2 17 Terminating DNASIS 1 From the File menu select Exit Chapter 3 Details of Analysis 65 Chapter 3 Analysis Functions 66 Details of Analysis 3 1 List of Analysis Functions DNASIS MAX supports the following analysis functions Analysis Category Analysis Button Name DNA Basic Complement Sequence Reverse Complement Sequence Reverse Sequence Translation Base Content Codon Usage GC Content Vector and Low Quality End Trimming DNA Search ORF Primer Design Oligo Probe Design Restriction Site Search Motif Search Searching a Motif Pattern Mutation Site Search Hairpin Loop Search Stacking Site Search Tandem Repeat Search DNA Comparison BLAST Search BLAST Search Protein DB BLAST Search Translation DB One to One BLAST Search Internet BLAST Search Internet BLAST Search Protein DB Internet BLAST Search Translation DB Smith Waterman Search One to One Smith Waterman Search BLAST Search and Extraction Clustering DNA Multiple Multiple Alignment Sequence Phylogenic Tree Multiple Alignment Tree View Creating Mul
289. ophilicity hydrophobicity and secondary structure for an amino acid sequence using parameters pertaining to the hydrophilicity hydrophobicity and secondary structure and then displays the results graphically Explanation of the Result Window e GH pome Yew ipo Deg BAANT ARS tAr Map View Hetephbery Sequence View Im irleleapes IInddalyny ivt E Pde 60 30 100 oral ver eer erer a anv ener R a Sarena pr annnasfelip psitliltse eve Map View This view displays the entire sequence graphically Sequence View This view displays the result of analysis for the specified table graphically The table name and average value are also shown at the center of the graph Selecting a Table AminoAcid Basic Analysis Parameterset Editor WM Hydrophabicity Hydrophobicity Table Hydrophobicity Hopp amp Woods z w alpha helix Chou amp Fasman beta sheet Deleage amp Roux Rcrophobicity Hopp Woo Hydrophobic ity Janin Hydrophobic ity Kyte amp Doolittle Hydrophobicity Rose amp Roy Window Size p I Amino acid usage I Isoelectric point e ceel 1 Click the Hydrophilic Hydrophobic Search button from analysis button view and an Analysis dialog box will appear Then click the Parameter button 142 Details of Analysis 2 In the Hydrophobicity Table field select a table you want to use The description of each table is then shown 3 Cli
290. ophycean_Mitochondorial Ciliate Macronuclear_and_Dasycladacean Echinoderm_Mitochondorial Euplotid Flatworm_Mitochondorial Invertebrate _Mitochondorial Mold Protozoan Coelenterate Mitochondorial Mycoplasma _Spiroplasma Scenedesmus Obliquus Mitochondor ial Standard Alternative Thraustochytrium_Mitochandorial Trematode_Mitochondorial Vertebrate Mitochondrial Yeast Mitochondrial 7 2 4 Running Translation Select DNA Bases from the analysis button bar then click the Translate button E and an Analysis dialog box will appear Click the Execute button to begin translation in the 3 forward reading frames Ezers ee alt gt pm m Oe owe e 2208 t 2 ae 83GB tees per s3ee e gt Sse usOwas nin bcm ed baba Displaying the Result of w A Translation Changing the Translated Amino Acid Notation from Three Letter to One Letter In the area for displaying the result of translation in the Sequence Editor view right click the mouse and select the Property menu The Parameter Setting dialog box appears From the Amino Acid Symbols field select One Letter and click the OK button As a result the amino acid sequence changes to one letter notation Translate View Property Show Frame Amino Acid Symbols FY eae dy tise pamecincimersiiasagingtion C One Letter AE T Frame 2 F Frame 3 C Three Letter Ala Glu The M Colorize map view Lox _ core Chapter 7 Tutorial
291. ored templates can be imported and displayed Export a Template 1 Select Command gt Export Template in the menu The dialog will appear Eh ual Seven My Donerer Jenom Py Pictures te ye fi retwd Gave awe m ype f Me hpa eer ar Cros 2 Type the file name and click Save to export the file to a template Import a Template 1 Select Command gt Import Template in the menu The dialog will appear tis Leek mr a My Docurere hom sere 2 Specify the file name and click Open and the template will be imported 282 Create Plasmid Maps 6 8 Exit Plasmid Map Drawing Click the on the Toolbar The editing window will close Chapter 7 Tutorial 283 Chapter 7 Tutorial 284 Tutorial 7 1 Before Starting the Tutorial 7 1 1 About Installation Using the Tutorial requires you to have sample data which you can install from the Sample Database using the following procedures From the Choose Destination Location window specify a location where you want to install the Sample Database which is installed in C HSK_DB for the initial setting Choose Destination Loost ioa Select folder Mere Sete will install files Please select Ouisbase directory lt Back Careri Choose Destination Location Window The Setup Type window then appears Choose the Typical parameter as how to install it Fatal Ghaid Woes Sulus Tyve Talect the Setup Type to install Click the ty
292. ot have aname DNASIS cannot export a restriction enzyme with this error Name the restriction enzyme and reexport it Complex Code Code list Not case sensitive Complex code ACGTT A A C C G G T U TorU R AorG Y C T or U W A T or U S CorG K GT or U M AorC B C GT or U D A GT or U H A C T or U Chapter 5 Databases 249 Complex code ACGTT V A C or G N A C G T or U Restriction Enzyme Data Format The restriction enzyme data you import or export must be plain text written in the following format To describe more than one restriction enzyme enter a carriage return before describing a next restriction enzyme HSK_REnzymeDB XXXX XXXX is the restriction enzyme name space not allowed within 255 characters NAME XXXX Restriction enzyme name space allowed SITE_N NN NNN Normal recognition sequence cut at SITE_C Complementary recognition sequence described for non palindrome structure Carriage return HSK_REnzymeDB XXXX XXXX is the restriction enzyme name space not allowed within 255 characters NAME XXXX Restriction enzyme name space allowed SITE_N NN NNN Normal recognition sequence cut at SITE_C Complementary recognition sequence described for non palindrome structure 250 Databases 5 7 Multiple Alignment Profile DNASIS MAX supports managing the profile of multiple alignments You
293. otif databases Name column Displays the name of the DNA motif database Any locked database shows a padlock icon to the left of its name You can click the column header to sort the databases by name of Motifs column Displays the number of motifs registered in the DNA motif database You can click the column header to sort the databases by number of motifs Modified column Displays the date when the DNA motif database was modified last You can click the column header to sort the databases by date Comment column Displays comments for the DNA motif database if any You can click the column header to sort the databases by comments New button Creates a new database Clicking this button causes a new empty database to be created and added to the list Delete button Deletes the selected motif database This button is disabled if no database is selected You cannot delete a locked database Property button Displays the properties of the selected motif database This button is disabled if no database is selected or if more than one database is selected The Nucleic Acid Motif Database Property dialog box appears View button Displays motif data from the selected motif database This button is disabled if no database is selected or if more than one database is selected The Nucleic Acid Motif Database dialog box appears Import button Imports a motif database from an external fil
294. ox Vector Name Select the vector you want to trim from the list You can select only one vector Cloning Site Select the cloning site for the vector you want to trim from the list You can select up to two items on the cloning site To select more than one cloning site item click each item in the list while holding down the Ctrl key Specifies the minimum length of a match between the vector sequence and input sequence to use the DP method to determine the portion of the vector sequence to trim If the matched length is smaller than this value DNASIS MAX will not assume the sequence is a vector sequence and will not trim Specify an integer of 15 or greater Specifies the minimum match ratio between the vector sequence and input sequence to use the DP method to determine the portion of the vector sequence to trim Ifthe match ratio is smaller than this value DNASIS MAX will not assume the sequence is a vector sequence and will not trim Specify an integer of 0 or greater Specifies the destination to output data if trimming results in a shorter sequence than the specified length If this check box is selected DNASIS MAX will output data to the Others folder lower folder If this check box is not selected DNASIS MAX will output data to the Trimmed folder upper folder If If vector trimming length is 0 bp is selected however that setting takes precedence Specifies the destination to output data if vector trimming is
295. p 1 is copied as shown below Sequence Sequence 10 20 30 40 AF165046 Sequence ttgggggcogc cactccacca tagaccacte ccctgtgagg aactactgte tte Untitled001 Sequence tatgagtgtc etgcagecte caggteccce cetcecegga gagccatagt get 70 80 90 100 110 AF165046 Sequence aagcetctag ccatezcgtt asiatgazte bogtecazco teodgetece cce Untitled001 Sequence accggtgagt acaccegaat teccaggate accegetcct ttottegate aac 130 140 150 160 170 AF165046 Sequence gagagccata stestctece gaaccestea etacaccega a ttgccagga tga Untitled001 Sequence atgocteg AF165046 Sequence etttettgea teaacecect caatgcctee acatttesec etecccecec gag 250 260 270 280 290 Chapter 2 Refer to Selecting Ranges in 2 7 Editing Sequences advanced Refer to About the Target in 2 9 Editing and Analyzing Multiple Sequences Refer to About the Target in 2 9 Editing and Analyzing Multiple Sequences DNASIS Basics 47 Creating New Sequences by Linking Noncontinuous Ranges of an Existing Sequence You can join several noncontinuous ranges of any sequence and extract them so that they can serve as another sequence This function is convenient for example when you want to select all ranges of the exon part before creating a new sequence by joining them 1 Select any number of ranges of any sequence as shown in the figure 10 20 20 Sequence TNAGGTCN NNAGGGCGNG NINNTGTGGN Annotation Experimental 9
296. plement SCQuene 225 icciseiceeccecesecnvedaceceszegeecusteietecduduascetetacedestasnsceasivgacdusnaece erecevssnsie 174 4 2 Reverse Complement Sequence cccceceeeeeseeeceeeeeeeeeeeaneeceeeeeseesseaeeeseeeseseesseaeeeseeeeneees 175 4 3 Reverse SOQUENGCE sisikii ce esece de cceerscentteceedeceeeet sient te seevedecteceeeee dees sastetenweteeedetattetieeieieents 176 ASA TPANSAUION EEATT ATTAT cusya achnubacts ues sanuesel uectcuayanestiobacck Cuavacmaetles tere evanae 177 A 5 Base Comte int r ect castes levee census leg EE a a a r a Ea aa are a Aa P aE AEn ianea cevevassuncdedesdevdvesd 178 AG Codon USaGe vite ssctviceisceveessseteecececctecssctensece ceceeveceuee cece cneers ceteveenecntenveetne case cutee NONN aiaia 179 Af GO COmte int sco caren nE cats NEA EAR A EE E EE A A E S 180 4 8 Vector and Low Quality End Trimming sssnsusseensnennnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 181 AO ORF A E T 183 4 19 Pamer Desig eriiirg a tria AEN EEA E EREA EAE EE ER 185 4 11 Oligo Probe Design sssssusssunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nennen 191 4 12 Restriction Enzyme Site Search ssssussssnunsuunnnnnunnnnnunnnnnnnnnnnnnnnnnunnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnn na 192 AIS MOtif SQAnC icccesecacecchececcees EAE AREY NEARE GEEAE REEE AEEA NA EEEE SR 194 4 14 Mutational Site SearCh sssssessesnenennennnnnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
297. ponds to the pwgapext parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter determines the probability of a gap being extended A larger value results in a shorter gap Protein Weight Matrix Corresponds to the pwmatrix parameter of Clustal W You can select BLOSUM 30 PAM 350 Gonnet 250 or Identity matrix which sets the value blosum pam gonnet or id respectively Alternatively you can select User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating similarity among amino acid molecules DNA Weight Matrix Corresponds to the pwdnamatrix parameter of Clustal W You can select UB or CLUSTALW 1 6 which sets the value iub or clustalw respectively Alternatively you can select User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating scores which specify whether DNA matches or does not match Gap Penalty Corresponds to the pairgap parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note When using a high speed algorithm use this parameter to specify the Open and Extension gaps The setting will not affect the processing speed unless you specify an extreme value K tuple word si
298. position of the inserting area Specified position Minimum value 1 Maximum value Plasmid base length number Insert end position Specifies the end position of the inserting area Specified position Minimum value 1 Maximum value Plasmid base length number Direction Selects the adding direction Clockwise forward Clockwise forward Counterclockwise backward Non direction When tabs other than the Annotation Tab are selected it is possible to change the line type and arrow color 2 Input necessary information and click OK The annotation will be added Also when the arrow overlaps with the existing arc arrow an arc arrow will be created outside the circumference Change the Plasmid Circle The size of a plasmid circle can be changed and moved by the mouse Drag the handle to change the size and the positions and sizes of the relevant figures also change Also when moving a circle the relevant figures are moved together The plasmid name and the text area for the base sequence can also be changed or moved but the text area cannot be deleted Figures can also be changed by changing the plasmid properties The operation is described below 1 Select a plasmid circle and click on the Toolbar The Plasmid Component dialog will open Chapter 6 Create Plasmid Maps 273 ass Component Prawned Live x Danet are Paene Same arge omw tomy Sart pore Degeri iidse 7 D
299. presenting A or G Y Complex code representing C or T W Complex code representing A or T S Complex code representing G or C K Complex code representing G or T M Complex code representing A or C B Complex code representing C G or T D Complex code representing A G or T H Complex code representing A C or T V Complex code representing A C or G Gap This can be entered only in the alignment display mode Entering Amino Acid Sequences 1 Select File gt New Menu and a prompt dialog will appear For Type select Amino Acid and for Content select A new sequence then click the OK button 2 Anew amino acid sequence is produced in the Sequence View 22 DNASIS Basics ialxi te OF pomo p toe SO ee 7B gt s326 t Dek as gt Dri Base Drin Seach Desh Compan Dabber oom T DAA gee Saguna Pran Area Bae js th 4 igam 4 o a g mj Target UrttiedEEC Poster se rare 3 Any character entered from the keyboard is inserted at the Insertion Pointer which is a vertical bar flashing at the laa point in the Sequence View You can also paste it from the Clipboard Characters You Can Use for Amino Acid Sequences The following is a list of characters you can enter in amino acid sequences CO Jaebrevaten pone a m e ooo E R Ag or SOS PN Asn Psparagine o Asp ema SSS pa Gin fwe SSCS pe Gu fwe SSCS A a m me em oo E
300. ps parameter of Clustal W Selecting the check box enables the parameter Note Specifying this parameter prevents a gap from being created at the end This parameter is useful for a sequence that is estimated as not important biologically Tree Make Multiple Mignenent Profile Parameterset Editor E xj General Pairmize lieriment NultipleAlierment ProteiGap Tres C Prybesnetic irea Bootstrap tree Number of bootstrap triste 1 10000 feod ro 1 1000 I Exchade positions with gaps I Corect tor multiple sbetitutions co Item Phylogenetic tree Coce Help Description Corresponds to the tree parameter of Clustal W Bootstrap tree Select this check box when evaluating the reliability of the tree using the bootstrap method Corresponds to the bootstrap n parameter of Clustal W 212 Details of Parameters Number of bootstrap Corresponds to the bootstrap n parameter of Clustal W Seed no Corresponds to the seed parameter of Clustal W Exclude positions with gaps Corresponds to the tossgaps parameter of Clustal W Correct for multiple substitutions Corresponds to the kimura parameter of Clustal W Chapter 4 Details of Parameters 213 4 24 Phylogenic Tree Using Profiles DNA and Amino Acid The parameters are the same as 4 23 Creating Multiple Alignment Profiles describes 214 Details of Parameters 4 25 Sequence Assemble Perametercet Nama
301. ption 100 Ahenment 100 Query Genetic Codesblastx onb Standard 1 bd Choose an organism trom the leet to limit your BLAST search none z or enter your organism name here Matrix PAM30 PAM 0 10 1 087 OSUMBO 10 1 087 BLOSUMSZ 11 1 035 default BLOSUM45 14 2 087 PAM30 7 2 090 zj Gap Existence cost Per residue gap cost Lambda ratio 9 1 087 3 From the Database Selection combo box select a database you want to search 4 Click the OK button Selecting the Species 1 Click the BLAST Search icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and the Internet BLAST Search Parameterset window will appear 2 Click Setting to display the NCBI Advanced BLAST Search window 114 Details of Analysis 3 From the Database Selection combo box select a database you want to search 4 Click the OK button Chapter 3 Details of Analysis 115 3 21 Smith Waterman Search This function provides high precision homology search using the Smith Waterman algorithm between the input sequence and the target database The optional GENE BRIGHT III board allows this rigorous similarity search to occur at a high speed on a personal computer Types of Smith Waterman Search There are two types of Smith Waterman search for DNA sequences Button name Description Smith Waterman search Performs a Smith Waterman search between a DNA sequence and a DNA seque
302. ption The window displays a list of proteolytic enzyme data registered in the database You can select one or more proteolytic enzymes and manipulate the data You can click the column header to sort the data in ascending L button or descending O button order for that column Initially data is displayed in ascending order of the enzyme name Acrosin Acrosin GathepsinB1 RIX GathepsinB1 GathepsinG LYF X CathepsinG Chymosin FIM Chymosin Chymotrypsind FYWIxX Chymotrypsina ChymotrypsinG FYL IX ChymotrypsinG Import Clostripain RIX Glostripain e A Enteropeptidase DDDDK I Enteropeptidase Ficin RIX Ficin PE AE TENSE CE E ma PE P ERINE PER P Item parameter Description Name NAME The name of the registered proteolytic enzyme Recognition Sequence SITE Sequence recognized by the proteolytic enzyme An amino acid sequence is represented in the single character format with an exclamation mark indicating a cut position If there is more than one recognition sequence a slash is used as a delimiter If there is more than one recognition amino acid complex code each is enclosed by brackets X indicates any amino acid Example KR X AR X Identify KX RX and ARX and cut between K and X R and X and AR and X Comment Displays comments for the proteolytic enzyme if any New button Creates new proteolytic enzyme data The New Enzyme dialog box appears Delete button Deletes all selected p
303. quence name the cluster name to which the sequence belongs the homology score with the cluster representing sequence and the input data sequence The longest one of the sequences under the same cluster is chosen as the cluster representing sequence Data narne Format toolbar m _ AoD Output Data button Menu a ge vee p ie Bj aj Hif AZ Column header rarer 7 ADA TTTC TTC TOA AANI TACATAAAA TO LAG TOOTOO TOE TORRE TOO DAA y Cells VAN AAT ATAAAATO 7 in yay ny TREO ADATTO ATT 120 ACAGACAANATTATAY j TOOAOAADAOCTTHI TAT TADAADOAT OAO TODON TCT wa num Status bar Cells The following shows how to select cells Itis the same method as how to operate the Excel program Select a particular column Click the column number Select a particular row Click the row number Select all cells Click the Select All Cells button SelectAll Cells button Select a range of neighboring cells Click the upper left cell of a selection range Then while holding down the Shift key click the lower right cell Select a range of non neighboring cells Click the first cell Then while holding down the Ctrl key click the subsequent cells 132 Details of Analysis Each time you double click the column header the cells are sorted in ascending or descending order can edit cells but cannot save them Output Data Button The button is not used for this analysis Grid Viewer Menu File menu E
304. quence or import one from an existing file 2 It is possible to select either a DNA sequence or amino acid sequence For selecting a DNA sequence click from the View Toolbar For selecting an amino acid click m 3 To remove a sequence from the search right click over the sequence name 4 Then select Hide from the popup menu The sequence will be hidden and only the search target sequences will display in Sequence View Select Species Select a target species for the Homology Search 1 Click the Options item from the left hand vertical menu 2 Click the GeneIndex Homology Search icon then click the Parameter button in the Analysis dialog box that appears Select the target species and click OK Perform Homology Search 1 The target sequences for the search will display in Sequence View 2 Click the Option tab from analysis button view and click the GeneIndex Homology Search icon Chapter 3 Details of Analysis 169 oe Untitled DNASIS Bae ald x Bile Eck swewe yew Heb JO Ss R tRe o SAAB e al Aaael s sBlt et slli oan snaa ea ee he Gl SE DNA Basio aran AF087301 3 71 bp Chlaxydia trachomatis 344 transaldo DNA Search A AFOG7301 DNA mode Button laaene ses nore eee VERSI OJ F007201 1 GI 4140495 oops Chlaxydia trachomatis AminoAcid mode Aminohcid Basic Button AminoAicid Search AminoAcid Compare Aminaicid Mubigle Sequence Database Options Sr DNAS pace
305. quence0026 0 072 0 041 0 147 0 205 Sequence0015 0 179 Sequencel 14 Sequencel0 16 0 030 0 138 0 013 squencel 002 0 127 Sequence0029 r0 090 Sequence0017 0 053 Sequence002 Sequencel021 This result window uses the Phylogram format where the sequence name is displayed on the right at the end of each horizontal line and the evolutionary distance is displayed at each branch point The length of each horizontal line is proportional to the evolutionary distance File menu Export Explanation Saves input data as an external file that is given a name Export Tree Names and stores the phylogenic tree data in DND dendrogram format Save Saves the currently displayed data by overwriting the original data Note At present this function is not available Save as Saves the currently displayed data by using a different filename Note At present this function is not available Print Performs printing Print Preview Confirms the image of printing If you click Close you can exit from the Print Preview mode and return to the original display mode Print Setup Sets the size of printing paper Exit Closes the window Edit menu Explanation Undo Cancels the previous edit operation Copy Copies the image of a phylogenic tree into the Clipboard OutGroup Starts the edit command Set an Out Group
306. quences Corresponds to the maxdiv parameter of Clustal W Note This parameter prevents DNASIS from aligning sequences having distant relationships until it aligns the sequences having the closest relationship DNA Transitions Weight Corresponds to the transweight parameter of Clustal W Note This parameter specifies a value of 0 or 1 for replacement If0 is specified DNASIS does not assume replacement asa match If 1 is specified DNASIS assumes replacement as a match You should specify 0 for closely related DNA sequence data and 1 for distantly related DNA sequence data Protein Weight Matrix Corresponds to the matrix parameter of Clustal W You can select BLOSUM series PAM series or Gonnet series which sets the value blosum pam gonnet or id respectively Alternatively you can select User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating similarity among amino acid molecules DNA Weight Matrix Corresponds to the dnamatrix parameter of Clustal W You can select IUB or CLUSTALW 1 6 which sets the value iub or clustalw respectively Alternatively you can select User defined to have DNASIS use the matrix file specified in the edit box Note This parameter specifies a table indicating scores which specify whether DNA matches or does not match Use negative matrix Corresponds to the negative parameter of
307. r 3 Details of Analysis 69 3 3 Reverse Complement Sequence This function converts DNA sequences into complement sequences converts them into reverse sequences and then adds the converted complement sequences as new sequences Explanation of the Result Window th Gh iemeree Yew th i B DEU gt vee 6QOt8 aR sG gtt i o es 232 Ben as Map View Sequence View w aar mace sef Sequenee TGTNAGGTCH NNAGGGOGNC traeo eef_RC Sogan NAACCTNCNC TGATNCGCCT Reverse Complement Sequence Sequence View The reverse complement sequence is displayed below the specified sequence The sequence name consists of the original sequence name followed by _RC Example If the sequence to be analyzed is ACTTGAGAT clicking the Reverse Complement Sequence button converts it to ATCTCAAGT 70 Details of Analysis 3 4 Reverse Sequence This function converts DNA sequences into reverse sequences and then adds them as new sequences Explanation of the Result Window Map View Sequence View POS eeeT eee TONDO ane eee e eet Enea Tere purer ererer N a Lema Saausnos TOTNAGGTCN NNAGGGCONC ante on trace wet_h Sequence METOGANGNS ACTANG Reverse Sequence Sequence View The reverse sequence is displayed below the specified sequence The sequence name consists of the original sequence name followed by _R Example If the sequence to be analyzed is ACTTGAGAT clicking the Reverse Sequence bu
308. r button m Use hput Pattern A Help OK Cancel 2 Place a checkmark in the Use Input Pattern check box and enter a pattern you want to search for 3 After selecting Use Input pattern and entering desired pattern in the text box click the OK button 4 Analysis Result View shows a motif if found with the name of Input_Pattern Creating a Motif Database 1 Click the Motif Search Amino Acid button from analysis button view and an Analysis dialog box will appear Then click the Parameter button 2 Click the Setting button Amino Acid Motif Database Manager appears 3 Click the New button A database named Untitled is created in the window 4 Double click Untitled The Database Property window appears Chapter 3 Amino Acid Motif Database Property Database Name funtiied of Motifs D Last Modified Date 2001 9 6 Comment 5 Make settings according to the following contents of the window Database Name Name of a database to be created I DB Lock Details of Analysis 145 DB Lock When checked this item prevents motifs from being added or deleted or prevents a motif database from being deleted of Motifs Number of motifs registered with the database Last Modified Date Date on which data was last modified Comment Comment given to a database 6 When you complete the selection click the OK button database Adding Motif Data This concludes the process of creating
309. r selected cells in a file as tab delimited text Adding a Motif Database You can add a new database to the motif database For details refer to Adding a Motif Database in 5 5 Amino Acid Motif Database Browsing the Detail of the Found Motif In the Sequence View or Map View double click the motif to display its details 100 Details of Analysis Nucleic Acid Motif Annotation Chapter 3 Details of Analysis 101 3 15 Mutation Site Search This function searches for restriction enzyme recognition positions such that on a per frame basis a one base replacement will not affect the result of translation but prevent a cut by that restriction enzyme The resulting DNA sequence with information about such potential mutation sites is displayed in a new window Explanation of the Result Window File Edit View Help 6997 x MUTATION SITE SEARCH 3 Codon Table Name Universal Frame No Enzyme NAME Find Position Mutation Seq MUT Pos Recognize Seq CUT Pos Translation 3 EcoH 188 192 gcggg 188 lccsgg 187 cce gt ecg P 2 EcoH 208 212 gccgg 208 lccsgg 207 cgc gt cgg R 3 EcoH 230 234 gccgg 230 lccsgg 229 lccc gt ccg P f 2 EcoH 288 242 gcc 238 Iccsgg 237 ggc gt sgs G 1 EcoH 294 298 gccgg 294 loesgg 293 ccc gt eeg P 2 EcoH 319 317 tcggg 313 ccsgg 312 ctc gt ctt L 2 EcoH 358 362 gcggg 358 lccsgg 35
310. r the EMBL Nucleotide Sequence Database The part ranging from an ID line to the point immediately before an SQ line is read as a comment while the part ranging from the SQ line to is read as a 26 DNASIS Basics Refer to 2 14 Waveform Display Mode sequence The first accession number on the AC line is used as a sequence name If there are no accession numbers the first word on the ID line is used as a sequence name How to distinguish DNA and amino acid If the ID line includes characters DNA or RNA it is regarded as DNA Also it is possible to analyze Features and show as annotations If sequences are separated by a line in a file all of those sequences are read into and displayed in one project In this case a dialog box titled Import List will display the list of individual sequences allowing you to select those to be imported Reading Files in the PIR Format This is a standard format for the PIR International Protein Sequence Database PIR PSD The part ranging from an ENTRY line to the point immediately before a SEQUENCE line is read as a comment while the part ranging from the SEQUENCE line to is read as a sequence The first word on the ENTRY line is used as a sequence name Any sequence including Type Protein on the ENTRY line is regarded as an amino acid sequence otherwise the sequence is regarded as a DNA sequence Also it is possible to analyze Features and show as
311. re Engineering Co Ltd Windows is a registered trademark of Microsoft Corporation NCBI and BLAST are software products developed by the National Center for Biotechnology Information Primer3 is a software product developed by the Whitehead Institute for Biomedical Research All other company and product names mentioned in this manual are trademarks or registered trademarks of their owners Under the approval of UK Medical Research Council our waveform display program uses the io_lib library developed by Staden Package of the U K The Multiple Alignment method uses the EMBL licensed ClustalW The plasmid mapping function uses the library of Rogue Wave Stingray Studio and with the consent of Rogue Wave Software Inc Hitachi Software Engineering Co Ltd reserves the right to make changes without notice to this publications as well as to the software it describes Information concerning products not manufactured or distributed by Hitachi Software Engineering Co Ltd is provided without warranty or representation of any kind Hitachi Software Engineering Co Ltd will not be liable for any erroneous or incorrect descriptions in the manual xiv Preface Technical Support Information United States MiraiBio Inc 1201 Harbor Bay Parkway Ste 150 Alameda CA 94502 USA Only 1 800 624 6176 Tel 1 510 337 2000 Fax 1 510 337 2099 www miraibio com gene miraibio com Europe Hitachi Software Engineering Europe AG Neues Kr
312. re on the trace data De pe pome ye ie OSG roe GATOR njegstenRyd HET HOMACGCT S E D boe ATTTTICTOAATCTCTATTOAATT CCAATT AAAATACCAAGATTTWCACATACAATGACATCATT ome joe E N 58 DNASIS Basics Switching between Waveform and Sequence Displays You cannot analyze sequences in the waveform display mode In that case you need to switch to the DNA display mode To display a sequence click the button on the View Toolbar To display a waveform click the button on the View Toolbar The method of a range selecting sequence is convenient because the selected range interlocks two modes the DNA display and the waveform display Selecting Waveforms to Be Displayed You can display only specified waveform when there are several waveforms that have been read 1 Click the button on the View Toolbar to display the dialog box showing the list of analysis results H 2 Look for and select a line in which the Data Name field shows the data name and the Analysis Name fields gives Trace 3 To display the data click the Show button To hide it click the Hide button 4 Press the OK button Double clicking the header for the Analysis Name filed in the list of analysis results causes the results to be sorted according to the order of the analysis names This function can be conveniently used when you want to select a line Click while the Shift key is held down to select a range Click while the Ctrl key is held down to select mor
313. res to copy the graphics 1 Drag a waveform to select a range 2 Right click to display the pop up menu 3 Select Copy 4 Paste the copy into another application such as MS Word as shown in the figure Chapter 2 DNASIS Basics 61 ee be oe be ee ee oe ary agen 62 DNASIS Basics 2 15 Saving Sequences as Text Files You can output the sequences currently displayed in the window as a file with the FASTA format 1 In the Sequence View select a sequence you want to export 2 Select Export from File in the menu SE I I 2 xi Saen amp Hsk oe x ck Ee C TutorialData L BlastDB Ci vectorData GenomeDB MultipleAlignmentProfile _ NAMotifDB SequenceDB File name Save as type Fasta fal x Cancel Target Sequence Range Current sequence amp All All sequences in a file C From Tol bp C All sequences in separate files 3 Enter a file name and click the Save button Chapter 2 DNASIS Basics 63 2 16 Copying Images You can copy all the graphics displayed in the Map View or Sequence View into the Clipboard Since these graphics are actually copied as vector data you can paste them to another application such as MS Word and produce a high resolution printout 1 Click any blank part in the Map View or Sequence View to switch to the active mode 2 Select a range you want to copy using such operations as expanding shrinking and scr
314. responds to the nopgap parameter of Clustal W Selecting the check box enables the parameter Note Specify GapPenalty for each amino acid A gap is likely to be inserted where many amino acids are set in the sequence data Hydrophilic gap off Corresponds to the nohgap parameter of Clustal W Selecting the check box enables the parameter Note Specifying this parameter increases the probability that a gap is inserted if five or more hydrophilic amino acids are contained consecutively Hydrophilic Residues Corresponds to the hgapresidues parameter of Clustal W Note Specifying this parameter reduces the probability that a gap is inserted if gaps are too close to each other A penalty is given if gaps are closer to each other than the value specified here Gap Separation Distance Corresponds to the gapdist parameter of Clustal W End Gap Separation Corresponds to the endgaps parameter of Clustal W Selecting the check box enables the parameter Note Specifying this parameter prevents a gap from being created at the end This parameter is useful for a sequence that is estimated as not important biologically Tree MultipleAlignmentParametertditor E xj GeneralSettings PairmiseAlienmers MultipleAlienment ProsenGsp Tree Piylpeenatic iran C Bootstrap tree Number of bootetap triste 1 10000 fesd ro 0 1000 I Ekchde positions with gaps I Corect tor multiple sbstitutiong co Item Phylogeneti
315. riisitiai iti EAE EREE a EE 156 Selecting a Database to Be Searched excluding one to one BLAST search s s ssseisissrsrsrsreresre 156 3 38 Smith Waterman Search AMINO Acid cce ce ceseeeeneeeeeeeeseceeeseeeseseeesesneessseseneeeennes 157 Eypes O Smith Waterman Searho isses iisen scat uses aE E EEE E E E E OR EE 157 Explanation ofthe Result WindOw siicsc ccesv caseetestavesiene dctusacedviseastevaseacctanesqsteuueuacisusssactessoudcccaneavtene 157 Selecting a Database to Be Searched Smith Waterman search only ssssssssssssssrsrsrsrsrsrsrsrsrsrsrsrsrsess 157 3 39 Multiple Alignment AMINO Acid cccceesee secs ee seneeesneeseseeeseeseseeseseeeseseesasaesenneesennes 158 Explanation of the Result Window 158 Setting Criteria for Determining Match Bases 158 Analyzing a Selected Range oo 158 Creating a Consensus Sequence isco acacia tied E N E ocala 158 3 40 Phylogenic Tree Amino Acid Explanation of the Result Window Changing the Type of a Phylogenic Tree Changing the Font eee TA Displaying an Expanded Phylogenic Treeren nieis r i EAE ERRA Setting an QUueGroup o eean eA E AAEE EA AAA EA AES EA Ne OESE SPENE EREE E R Replacing Branches Evaluating the Branching Reliability Bootstrap Tree ssssesesesseessesrseseesesessrsrstsreseseserriserresessrsrseseese 161 3 41 Creating Multiple Alignment Profiles Amino ACiq 0 c cccsessseeeseeseseeessteeeneeeeesn
316. roteolytic enzymes Property button Lets you edit data for the selected proteolytic enzyme The Enzyme Property dialog box appears This button is disabled if no enzyme is selected or more than one enzyme is selected Import button Imports exported data for a proteolytic enzyme Export button Exports data for the selected proteolytic enzyme This button is disabled if no data is selected Help button Displays online help OK button Exits from the Proteolytic Enzyme Database Manager Creating New Proteolytic Enzyme Data In the Proteolytic Enzyme Database Manager you can click the New button to create new proteolytic enzyme data Clicking the New button causes the New Enzyme dialog box to appear Enter data in this dialog box to create enzyme data You cannot register an enzyme having the same name as that of any existing enzyme registered in the database 258 Databases New Enzyme Enzyme Name Recognition Sequence Comment p OF Cancel New Enzyme dialog box Item parameter Enzyme Name NAME Description Enter the name of the proteolytic enzyme you want to register The OK button is disabled if this field is blank Recognition Sequence SITE Sequence recognized by the proteolytic enzyme An amino acid sequence is represented in the single character format with an exclamation mark indicating a cut position If there is more than one recognition sequence a sla
317. rs in the data you have entered 1 The Enzyme Name text area does not contain a restriction enzyme name 2 The Normal text area does not contain a recognition sequence 3 The Normal text area contains a character other than ACGTURYWSKMBDHVN and 4 The Normal text area does not contain an exclamation mark or it contains more than one exclamation mark 246 Databases Item parameter Description 5 The Complementary text area contains a recognition sequence including a character other than ACGTURY WSKMBDHVN and 6 The Complementary text area contains a recognition sequence without an exclamation mark or more than one exclamation mark 7 The Complementary text area contains a recognition sequence having a length different from that of the sequence in the Normal text area When you click the OK button DNASIS checks for a duplicate enzyme name If the database already contains a restriction enzyme having the same name DNASIS shows a dialog box with a message stating that the restriction enzyme name is a duplicate and you cannot register the restriction enzyme Cancel button Cancels the creation of a new restriction enzyme and returns to the Restriction Enzyme Database Manager window Importing Restriction Enzyme Data Import file dialog box In the Restriction Enzyme Database Manager window clicking the Import button causes the following dialog box to appear joven eee vx Lock joc ad My Docum
318. rue Brevigus Next coe 2 To change the font use the Display Font Name field To change the size use the Display Font Size field 3 At the end of the setting operation click the OK button to display a phylogenic tree in a new setting Displaying a Magnified Phylogenic Tree 1 Click the Q icon on the toolbar to make the mouse cursor look like a magnifying glass Chapter 3 Details of Analysis 123 Sa Sees RACOT 2 Click or drag any section you want to magnify The specified section can be expanded To reduce it click the E button and perform a similar operation You can return the displayed item to its original size by clicking the 7 button Setting an Out Group You can set a selected branch as an out group 1 Click the D icon on the toolbar to change the mouse cursor to the mark E eA OA 2 Move the cursor onto a branch you want to set to an out group and click it The specified branch has now been set in the out group Exchanging Branches You can exchange branches 1 Click the G icon on the toolbar to change the mouse cursor to the mark E tea omz nal 2 Move the cursor to a branch you want to exchange with another within a tree and click it The specified branch is replaced and displayed Evaluating the Branching Reliability Bootstrap Tree This function evaluates the reliability of a tree form using the bootstrap method 1 Click the Phylogenetic
319. ry notices that are on the original copy of the Software provided to you Certain Software however may include mechanisms to limit or inhibit copying Such Software is marked copy protected e Transfer of the Software and all rights under this Agreement to another party together with a copy of this Agreement if the other party agrees to accept the terms and conditions of this Agreement If you transfer the Software you must at the same time either transfer all copies whether in printed or machine readable form to the same party or destroy and copies not transferred RESTRICTIONS You may not use copy modify or transfer the Software or any copy in whole or in part except as expressly provided for in this Agreement Any attempt to transfer any of the rights duties or obligations hereunder except as expressly provided for in this Agreement is void YOU MAY NOT RENT LEASE LOAN RESELL FOR PROFIT OR DISTRIBUTE License Agreement TERM This Agreement is effective until terminated You may terminate it at any time by destroying the Software together with all copies in any form This Agreement will immediately and automatically terminate without notice if you fail to comply with any term or condition of this Agreement You agree upon termination to promptly destroy the Software together with all copies in any form LIMITED WARRANTY Mirai warrants for the period of ninety 90 days from the date of delivery of the Software to you as e
320. s the DNA multiple sequence and the amino acid multiple sequence If you click the analysis button while holding down the Ctrl key the analysis covers all the sequences that are currently displayed n atesi 50 DNASIS Basics 2 10 Searching for Sequence strings Refer to About the Target in 2 9 Editing and Analyzing Multiple Sequences Searching for Sequence Strings Using a character string this function searches for a string in the sequence being edited 1 Select Sequence and then Find or click the button on the toolbar 2 The following dialog box appears Find eix Fidh OSSSOSCSCS Find Find Way Normal Direction Down Find 4 Find Range Current Sequence I Marker em Help 3 Enter a character string you want to search for in the Find What field 4 Click the Find button 5 Ifa match occurs the window automatically scrolls to the range of the match The search process is case sensitive uppercase and lowercase characters are distinguished Search starts at the point where the Insertion Pointer is currently located or at the point following the selected range Jumping to the Next Match To jump to the next match select Sequence and then Find Again or press the F3 key To go back to the previous match press both Shift and the F3 key at the same time Selecting All Matches at Once 1 Select Sequence and then Find or click
321. s a new DNA sequence Replacing the Trimmed Part with N 1 In the analysis result for trimming click all the bars indicated with Trim Always Low Quality and Vector xxx to select them Ifyou want to select more than one item click the second and subsequent items by pressing the Ctrl key 2 Click the IN button on the toolbar 3 The trimmed portion is now replaced with N 84 Details of Analysis 3 10 ORF This function searches DNA sequences for open reading frames ORF and displays the result Explanation of the Result Window La aiaia D pe pome p De Dsg BPS TIOp 4 2 48 e 236 e 2 22 ss 27 gt SS VAONA DMA Bese iwa Semen Map View Sequence View Sequence View This view displays the result of searching for ORFs together with the sequences The symbol on the bar indicates a start codon and the gt symbol indicates a stop codon If you click an ORF between the start and stop codons the ORF is selected and highlighted by the predefined color Map View This view displays the result of searching for ORFs under the sequences The symbol on the bar indicates a start codon and the gt symbol indicates a stop codon If you click an ORF between the start and stop codons both the ORF and the sequence in the region are selected Changing the Codon Table 1 Click the ORF icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and a P
322. s to a text file Using a text file you created with this feature you can import the profile to DNASIS running on another machine Profile Path Allows you to view or modify the path of the directory to store the profile Help Displays online help OK Saves the changes and exits from the Multiple Alignment Profile Manager Property Window In the Multiple Alignment Profile Manager clicking the Property button opens this dialog box Multiple Alignment Profil Name TESTAA Last Updated 2001 8 10 Sequence Kind Amina Acid z Total number of sequences 3 I Read Only Comment Test Profile Item Description Name Displays the name of the profile You can edit the name You can use up to 64 characters excluding any of the invalid characters lt gt You cannot specify the same name as that of an existing profile Last Updated Displays the date on which the profile was updated last Sequence Kind Displays the sequence type DNA or Protein of the profile You can modify this item only when the Total number of sequences is 0 Total number of sequences Displays the number of sequences contained in the profile Read Only Check this item if you want to prevent this profile from being overwritten Comment Displays comments for the profile ifany The comments cannot exceed 32767 characters You can use any single byte characters and carriage returns
323. search conditions requires you to set logical operators that connect condition equations Operator Format Description AND lt condition equation 1 gt Searches for the entries meeting all condition equations connected by an AND AND operator lt condition equation 2 gt OR lt condition equation 1 gt Searches for the entries meeting either of the condition equations connected by an OR OR operator lt condition equation 2 gt Join Conditions Join conditions are used to set comparative operators between the items and values of condition equations Joining condition Description is Searches for the entries having the same value as the setting in the Value Input field Ifa word is entered the entries that exactly match the whole word are hits partial matches are ignored Entering two or more words means that they are considered to form a phrase therefore the entire phrase is the candidate for a hit is not Negates the meaning of the verb is that is searches for the entries having a value not equal to Chapter 3 Details of Analysis 165 the setting in the Value Input field begin w Searches for the entries having a word that begins with the character string specified in the Value Input field Entering more than one word will result in improper search dose not begin w Negates the meaning of the verb begin w Option Setting Dialog Box Ux URL of NCBI Erie Is Maemum Erines 200 m a
324. seeeseaeseeeseaeseseseeeeeeeeees 62 2 16 Copying IMAGES iivicieccccssnisatin niin aveinni isa ciee NN A E aa oa aaa E 63 2 17 Terminating DNASIS iiss scccatissiieitaescivdnaia deciaetaecenanaseuedinaasueWanasucaciadaedanssbsventssagadaventdnsediazees 64 Chapter 3 Analysis FUNCTIONS ee eee ti i in i in i ieee eeeeeeeeeeeeeeeeeeeeeeeeeeeeeneeees OO 3 1 List of Analysis Functions cccceseeeeseseeeeeeeeeeeeeeeeneeeeeeeneeeeeeeeeeseseeneeseseeneesesesneesesesneeeneeenaees 66 3 2 Complement Sequence i e ose cee esss Seavssecveede da siuntsnstuvcvesiscvastasseeee adesentinctiertensaseastnctenestavssantieey 68 Explanation ofthe Result Window resien r R EA EE E E vested EE coun steers EE R E aE 68 3 3 Reverse Complement Sequence Explanation of the Result WIndows aian A RR EE RERE E R E RRR ERRER 3 4 Reverse SCQUCINCE siisii unimini aime asandan aeneae aweccdectienestedeenctaciecnverecdeacceeaesaedteecenecee Explanation of the Result Wido Wasan neea i ER R REE 39 5 TranslatiON wisi evcacascantavava ce veabievedvaadiaveuadiavwintecacavasbasteinte sheds addaucebteasiavabssvestouss otvvceadsavediveatinnaada 71 Explanation of the Result Window ccccessscessesseseceeceseeseeseeseesecaeceeeneeseeseeaececeseeseeaecaecaesereeaeeaeeateaeeates 71 Specifying a Framesto Display ssr scsssscsdssssecezscshecesess ieceuscshiceysssd cevssahdsevassiudaseeshdcasepaiicessanicepans TASR 72 Changinig to One Character Notation ii 5s ceisse
325. sequence editor view Each ORF is indicated by an arrow e a mmn cnm n oe Bre 24B7 a4 2325 vel3s7e0e Displaying the result of 7e 5 Dew as ORF search Decne damidmi If You Want to Change the Codon Table Click the ORF button and an Analysis dialog box will appear Then click the Parameter button and a Parameter dialog box will appear Under the initial setting Universal is found in the Codon Table of the Parameters item To change the Codon Table select another table from the drop down list and click the OK button Codon Table Universal zil e Alternative Yeast Ascidian_ Mitochondrial Bacterial and Plant Plastid E Blepharisma Chiorophycean_Mitochondorial Giliate Macronuclear Ciliate Macronuclear and _Dasycladacean E Echinoderm Mitochondrial Euplotid Flatworm_Mitochondrial lnverterbrate_ Mitochondrial Mold Mitochondrial Mold_Protozoan_Coelenterate_Mitochondorial Mycoplasma Mycoplasma Spiroplasma Plant Mitochondrial Protozoan Mitochondrial Scenedestims Obliquus_ Mitochondrial Standard Thraustchytrium Mitochondrial T Mitochondrial Vertebrate Mitochondrial Yeast Mitochondrial Code Similarly you can specify the start codon with the Initial Codon parameter 288 Tutorial Open Reading Frame Codon Table Universal aal Initial Codons Standard x Alternative Yeast Ascidian_ Mitochondorial Bacterial_and Plant plastid Blepharisma 1Chior
326. sh is used as a delimiter If there is more than one recognition amino acid complex code acids are enclosed by brackets X indicates any amino acid Example KR X AR X Identify KX RX and ARX and cut between K and X R and X and AR and X The OK button is disabled in the following cases For each sequence separated by a slash 1 There are more than one cut position 2 The data does not contain any amino acid characters 3 Any character other than A to Z and is used 4 Brackets are nested in other brackets 5 Brackets are not paired 6 Brackets contain X 7 Brackets contain no characters Comment Displays comments for the proteolytic enzyme if any OK button Creates a new proteolytic enzyme from the entered data DNASIS cannot register an enzyme if its name is already used for an existing enzyme In such a case you must change the name to register it Cancel button Cancels the creation of new proteolytic enzyme data Errors that may occur when creating new data Duplicate enzyme name If you specify an already registered name for a new enzyme the dialog box appears Click the OK button to return to the New Enzyme dialog box Change the name of the enzyme and retry tic Enzyme Datal se Manager dbtool Eg 1 Acrosin is already registered Please change enzyme name Editing Proteolytic Enzyme Data In the main window
327. si cse erriisis rri isrtri en I EV E TEE ESSENIS SSR 50 S arching Multiple Segu A S a R R 50 vi Contents 2 11 Aala lera to ar aaaea A E Gavuncbhcwaiida su eniaeeubnedagaa saluted ssndasisasnecdvesadis va saineasdneedeaca sstndued 52 About the Annota oina en EE RAAE ME RE A Aelita inns aaa aie 52 Creating New Annotations a roes rrine E VEs EEEE EEA EREE OEE REEE ORERE 52 Creating Annotation Entries tose veces ai anette g E NE EENE ERENT 52 Assigning Annotation Entries to the Range of Selection cies eceecseeeeseeseeetsesessceecseeeeeeeseeeeaees 52 Assigning Annotation Entries to Multiple Ranges of Selection at Once Editing Annotation Entries Deleting Annotation Entries AoA Deleting Annotations e e neccte caste neh eee ion oni da EEA ices enous AA 54 Creating Multiple Annotations asirni sess ssszisbss saseesssadsdeass aaeeea SEESE VEE EEEIEE VETA E EITSA NEEESE ESETERE 54 rA PA Ba AE AEA T EEE E TA TT E A EE A L O ETS 55 jina tata EITEAN AAN ET SARNA Tea A EEE EEE S E E E E TE E E Printing the Sequence View sed Printing Only the Current Range of Display essipessi iere ree iaeiae s 55 213 PROJOCUS E T TE T A ep thsctvevestsctes th selecsesvescertascuse essscvegiuselncetevecvustassuceteseey 56 About the Project y gscecsisccascssissecssdiccaasadeaseeesdccaiceanecesandsscascesndsesass acces vaveves ochavesnessdes sceusvucsacesavsseessivasecesaea tes 56 SAVING Projects ra celet tesco T E OEE ETE abe thea ease een namie nulls
328. ssword if the proxy server requires user authentication No Proxy Specifies a Web address that does not require any connection with a proxy server Use Proxy Server Uses a specified setting to connect to the Internet by way of a proxy server FTP Firewall Tab Internet Parameters xj HTTP Promy FIP Frewal Ma Server frewall dnase com Port a User Name arespace Password Type c c C USER user host gt PASS USER gt PASS gt USER user host Pacetve Mode Item Description Server Specifies the address of a firewall Port Specifies the port number of a firewall User Name Specifies the user name for connection to a firewall Password Specifies the password for connection to a firewall 14 Window Descriptions Item Type Description Specifies the type of a firewall that is to be used Passive Mode Makes a transfer in the PASV mode Mail Tab internet Parameters x HTTP Prony FTP Fuewai Ma Mal Address SMTP Server Por Item Mail Address anassa com omtp dras com Description Specifies the address of email SMTP Server Port Sets the SMTP server for sending messages Specifies the name of the SMTP server Specifies the port number of the SMTP server POP3 Server Port Username Password Sets the POP server for receiving messages Specifies the name of the POP3 server Specifies the port number of the POP3 server
329. storing public DNA sequences mainly GenBank wr This icon indicates that the database has been converted from a sequence database storing public amino acid sequences A This icon indicates that the database has been converted from a sequence database storing in house DNA sequences such as the experimental data available iH This icon indicates that the database has been converted from a sequence database storing in house amino acid sequences Kal This icon indicates that the database stores DNA sequences dedicated to BLAST search You can directly copy a file for example created by format db of the NCBI tool kit Ost This icon indicates that the database stores amino acid sequences dedicated to BLAST search You can directly copy a file for example created by format db of the NCBI tool kit Item Description Name Displays the name of the database of Seqs Displays the number of sequence data items stored in the database Source DB Source DB Displays the date on which the source sequence database was updated last Status Displays Empty or the last updated date Auto Update Displays Scheduled if automatic update is specified Button Description New Converts a database registered in the Sequence DB Manager to a database dedicated to BLAST search The Select Sequence Data Base dialog box appears However this button only creates an empty database without actually converting the database You must subsequently update it Delete
330. t click the button on the View Toolbar and respond to a dialog box that appears Deleting Sequences You can delete any sequence and its analysis result 1 Right click the name of a sequence you want to delete 2 From the pop up menu select Delete as shown in the figure AF165047 Sequence AF165048 Sequence AF165049 Sequence AF1ARNEN AFI Move Up Move Down AF165047 Sequence AF165048 Sequence AF165049 Sequence AF165050 Sequence 3 Selecting Delete will delete the sequence and its analysis result Once any sequence or its analysis has been deleted you cannot restore it Changing the Order of Sequence Display You can change the order in which sequences are displayed to provide an easier to read well organized result 1 Click the name of sequence whose order you want to change so that the sequence name is ready to be selected Chapter 2 Refer to Hiding Sequences in 2 9 Editing and Analyzing Multiple Sequences DNASIS Basics 49 2 Click the ita or pa button on the toolbar Alternatively you can right click the sequence name From the menu select Move Up or Move Down AF011752 AF011751 AF009606 AF011753 AFO4E AFOS Sequence Sequence Sequence Sequence Move Up Move Down Hide AF011 Delete AF01 AF009606 AF011753 AF046866 Sequence Sequence Sequence 3 This selection changes the sequence and its analysis result Even in the a
331. t Comments ei eeeeeeeeeeeee 28 Upper Limit on the Number of Sequences cececesceecseeseseeseeeeseeecseeseseeecsessesesseeseesaseecsesaeeesseeaseee 29 2 4 Editing Sequences basic eecccceseeceeeeeeeeeeeeneneeeesenseeeseeeseeesuaeseseseaeseeesaeseseseaeseseneanseeesees 30 About the Insertion POmtet twa ncn en Rata i ia asa ata 30 Ways of Moving the Insertion Pointer ecesceesesseeceeseeseeseesecseceeeseeseeaceaecaecesecseeaecaeceeeseeaeeaeeaeeneeeees 30 Contents V Inserting and Deleting Sequences eesis esi eroii ni Ee e R REAR EER ERRER 30 Pasting from the Clipboard sraon e EA ENN A E EE AAE E EE E E ane 30 Selecting the RANG aena oere E EREE E S EEEE E RRRS 30 Ways of Sel ctmga Specific RANGE sansoyo a E E E E 31 Canceling the Selections sa sssissech shes sesseics sect aein ee REEE E E A OSA TR 31 Deleting the Sel cted Ramee cies nra E R E E E aac A E 31 Replacing the Selected Ra penrai aE REE A EE E A AA EE 31 REMAINS SEQUENCES moniato a E ES E EEEE RE E EEE E S E EES 31 Restrictions for Naming Sequences Poen orara eiir aaa EEE EE AAEE ERA ARASA 32 2 5 Analyzing Sequences DaSIC ssssssssenssennnnnrnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nna 33 Analyzing SCQuenCes eterea a S ER lee ested A AAAA A E EAEE A EEEN E EEES 33 How to Display the Result of Analysis snn ea e E EEA E end 33 Customizing the Display of Analysis Results s sssssssesssese
332. t button Provides the same function as the Print menu Copy button Provides the same function as the Copy menu Help button Displays online help 76 Details of Analysis 3 7 Codon Usage This function displays the type and number of codons in DNA sequences The result of analysis is displayed in another window Explanation of the Result Window File Edit View Help B 6097 Univers Codon Usage Mode Start Position 1 Total Base Total Codon 1018 Other Codon 0 AminoAcid Count Percent 42 4 13 F F L L S S S Y File menu Description Export Exports the data in the window into a text file Print Prints the window Print Preview Displays a print image Print Setup Provides various print settings Exit Closes the result window Edit menu Description Copy Copies the data in the window as a tabbed character string into the Clipboard View menu Description Toolbar Toggles the toolbar to display hide it Status bar Toggles the status bar to display hide it Help menu Description About DNABasicAnalysisViewer Displays the version information of this analysis function in a dialog Contents Displays online help Button Description m Export button Provides the same function as the Export menu Print button Provides the same function as the Print menu Copy button Provides the same function as the Copy menu p Help button Displays online
333. t edit it OK button Saves the changes made to the motif data and closes the Amino Acid Motif Database dialog box This button is disabled if the database is locked Cancel button Discards the changes made to the motif data and closes the Amino Acid Motif Database dialog box Help button Displays online help Displaying Motif Properties From the motif list in the Amino Acid Motif Database dialog box see the previous section select the motif for which you want to display properties and click the Property button Motit Name S Motif Pattern IONE 27GF LIVMFY INTIR 18 PAI LIVMFY 2 5 LIVMFYC LIVMFY 210 Pattern Assistant z Motif Pattern Test Sequence i Motif Annotation ID aro SENEN DE 3 hydroxyacy CoA dehydrogenase si PA nd REI PAR FAI LSE NE Ge MERT Tiie REPEAT i iat ie r EEREEEFE PDOc00065 PS00067 3HCDH BEGIN EERE RERE RRRRRERRRARERREER t 8 hydroxyacy CoA dehydrogenase signature AKKER RKR RRR RRR RA ARR Ld DT iPr 1390 CREATED Lae 1995 DATA Hina NOY 1995 INFO UPDATE ure DNE x 2 i Gee ae x NT R x 3 PA LIYMFY 2 x 5 LIVMFYC 32 4934 0 Ost ives 1111 UNKNOWN 0 0 FALSE_POS 0 0 Help Cancel Details follow Item Description Motif Name Name of the motif You cannot edit this item if the database is locked The motif name must not exceed 255 characters Motif Pattern Pattern of the
334. t species for the Motif and Domain Search 1 Click the Options item from the left hand vertical menu 2 Then right click the GeneIndex Motif and Domain Search icon and select Parameter Select the target species and click OK Perform Motif and Domain Search 1 The sequences you want to search will display in Sequence View 2 Click the Option tab from analysis button view and click the GeneIndex Motif And Domain Search icon Ez Untitled DNASIS EE lgl Ele gdt Sequence yowe teb CETATI EErE EEUE is aatas DNA Base win yeast Saccharonyces cerevisiae lk m Ji go i gt te a R ita t ai amp t DNA Seach DNA Compare DNA Multiple Sequence ArinoAcid Basic ArrincAcid Search Arino cid Compare Arrino cid Mukigle Sequence Eia TONAS pace Automaticn ES Contig Manager e Geneindex Homology Search Gendirdex Mobi ard Domai Sas Juanan a Ready Target porin yeast Saccharomyces Position 1 aa 3 Click the Execute button from the Analysis dialog that appears Chapter 3 Details of Analysis 171 xi 5 Genelndex Homology Search Comment Conduct Homology Search in Genelndex Launch parameter editor to change species J Execute analysis without showing this dialog gt Ei Parameter Execute Close 4 A browser will open and connect you to the GenelIndex site A database selection page will appe
335. t the parameters refer to the NCBI Web site Advanced BLAST Chapter 4 GEN Fout Sequence Type Matric Fitial Gap Extention Gap Max Nun of Return F Qa Oli Score Target Databaze HSK SWoeeq NA br House NA MAM fab DNA DNA ma ae 7 4 oe FA Details of Parameters 201 Select All Desset A Setting Hep Otau ok Garcet_ Item Calculate by Description Specifies whether calculation based on the Smith Waterman algorithm will be performed using the GENE BRIGHT III board or using software GENE BRIGHT III Use the board You can select this item only when the board is available Selecting this item displays the number of boards installed on the machine Software Emulation Performs calculation using software without using a board Calculation by software will require very long time Therefore you should not select this item for a large database for example containing one million entries Input Sequence Type Specifies the type of the input sequence DNA The input is a nucleic acid sequence Amino Acid The input is an amino acid sequence Matrix Specifies the matrix used to calculate a score Initial Gap Specifies a penalty score for inserting a gap The value must be an integer between 16 and 0 inclusive and must not exceed the setting of Extension Gap Extension Gap Specifies a penalty score for extending a gap The value must be an integer bet
336. t was set here DNA Sets the sequence type to DNA Amino Acid Sets the sequence type to Protein Content button Sets the sequencing method New Sequence Makes a new DNA or amino acid sequence Sequences from files Imports sequences from a file Retrieving sequences from database Imports sequences from a sequence database If you select this and click the OK button a Select Sequence Database dialog will appear Retrieving sequences from NCBI Entrez Obtains sequences from NCBI Entrez If you select this and click the OK button an Entrez Search dialog will appear Open Existing Project button Select this radio button if you will open an existing project Open project Up to 15 recently used projects will appear To import a project not in the list select Other file then select the file you want from the file dialog To import a project not in the list select Other file then select the file you want from a standard file dialog Help button Opens the online help in a new window OK button Closes the dialog after the parameters have been set with the values entered in the dialog Exit button Closes the dialog without updating the parameters Closes the application when it is running Importing Sequences from a Sequence Database To start select the Retrieve sequences from database button then click the OK button Chapter 2 DNASIS Basics 19 Refer to the seq
337. tab delimited text Import Annotation Imports annotations Export All Annotation Exports all the annotations Export Selected Annotation Exports the selected annotations Print Setup Sets the paper size to use for printing 224 Details of Parameters Print Starts printing Edit menu Description New Annotation Adds new annotations Opens the Annotation Setting dialog Edit Annotation Edits the selected annotation single selection only Opens the Annotation Setting dialog Delete Annotation Deletes the selected annotations Copy All Copies all the annotations to the clipboard as tab delimited text with headers Copy Selected Copies the selected annotations to the clipboard as tab delimited text with headers Check All Checks all the annotations Check Selected Checks the selected annotations Uncheck All Unchecks all the annotations Uncheck Selected Unchecks the selected annotations Select All Selects all the annotations Help menu Description Help Displays online help Toolbar ed 5 47 Gal leh Ole Description The same as Save As All from File in the menu The same as Import Annotation from File in the menu The same as the Export Annotation from File in the menu The same as the Print from File in the menu The same as New Annotation from Edit in the menu The same as Edit Annotation from Edit in the menu The same as Delete An
338. tails of Analysis 87 Creating Amino Acid Translated Sequence for an ORF 1 Click the ORF button to search for ORFs 2 Click the Translate button to start translation 3 Click the desired ORF Then the result of translation is selected 4 Click the Amino Acid Transfer Button on the toolbar The window switches to the Amino Acid mode A new amino acid sequence representing the desired ORF is created in amino acid view of this project Ld SOF GRABS 28 SI ttet Li vor 33aea 88 Details of Analysis 3 11 Primer Design This function designs PCR primers Explanation of the Result Window Be oa poro jw tee osu see 6241752 7H ESE anwas OA boe DNA Segih Sequence View Q Raols Blt e t f Product Primer Sequence If you click the primer or product the sequence is selected a dialog box Displaying the Primer List For the primer design result in sequence view select the sequence name and analysis name then click the Result List Dialog button E 60 068 50 000 3 00 3 00 accecctecttttctassca 5 2774 20 69 679 60 000 4 00 0 00 ccectataaccacstttcca J Product 2571 2774 204 acccoctoct tt ictaagcagcateaatsazcat eat eezeacttac Pair 3 00 0 00 T Left 2570 2583 20 80 068 65 000 3 00 2 00 cacccoctocttttctaage Riet 2755 2774 20 69 67
339. teece ttaetateae betcetecas cotccazeac tcttcacgca gasagcetct azecatesce ttaetateae teteetveds cctccagece 130 140 150 160 170 E mo0001 Sequence mo0002 Sequence mo0003 Sequence M00004 Sequence ccccoctcce gesasascca tastectcte cesaaccesl Eaetacacce gaattgccag cccccctccc gesasaccca tastectcte cesoacceel Eaetacacce caattecces Gecccctece gesasaccca bastectcie cesaaccest Eaetacacce gaattgccag cccccctcce sesacaccca Pastectcte cesaacceet EaEtacacce zaatteccaz mo0001 Sequence mo0002 Sequence mo0003 Sequence M00004 Sequence gacgaccgge toctttctte gataaaccog ctcaatecct ggagatttgg gogtgccccc gaagactese toctttctts gataaaccca ctctatgcce ggccatttes ecetgccece saceaccege tectttctts sataaaccce ctcaatecct ggagatttgg eceteccece saceaccege tectttctts gatcaatcce ectcaatecc tggagatttg esceteccec 2 On the Switch Pane Toolbar click the Sequence mode so that sequence analysis and annotation entry tools become active Now you can analyze of the region of the alignment you highlighted in step 1 Meaning of the Background Color and How to Change It The result of a multiple alignment is color coded according to the degree of conservation of the individual bases across all aligned sequences You can change the matching rate and color combination 1 Click in the View Preference menu or click the gq button on the toolbar to open the Preference dialog box 2 Click the Sequence tab xj Font Sequence Foiding Fiuler Onghay Mode DNA
340. ters so that they are not replaced N can be replaced with A C G or T Accordingly TCN can be replaced with any of the following TCN TCA TCC TCG and TCT TCN TCA TCC TCG TCT Using the replaced character string the function searches the Codon Table again to perform atranslation The first TCN does not exist The next TCA can be translated into the amino acid of S No 19 in the table Similarly TCC is translated into S No 18 in the table TCG into S No 20 in the table and TCT into S No 17 in the table Because all the four Ss are the same amino acid TCN is translated into S Specifying a Frame to Display 1 In the Sequence View right click in the result of translation and select the Property menu 2 A frame names are displayed in the Frame field in the Translate View Property window as shown in the figure Place a checkmark in the check box of the frame you want to display Translate View Property Amino Acid Symbols C Ore Letter A E T V Frame 2 M Frame 3 Three Letter Ala Glu Thr Amino Acid Colors M Colorize map view Chapter 3 Refer to 5 8 Codon Table Details of Analysis 73 3 Click the OK button Changing to One Character Notation You can select a one character or three character notation to display the result of translation 1 In the Sequence View right click in the result of translation and select the Property menu 2 Select One Letter
341. the amino acid sequence once again 7 2 7 Running Amino Acid Motif Search After selecting the Amino Acid Search group on the analysis button bar click the Motif Search button S D Chapter 7 Tutorial 291 The search is performed according to the motifs that are registered with the amino acid motif database The results are displayed below the sequence in the Sequence View window and in the Map View window OSE PBF CA AST BRL HPI tte 2 WL vor szaag eae an In the area displaying the result of amino acid motif analysis double clicking the motif name causes motif information to be displayed 292 Tutorial 7 3 BLAST Search This section demonstrates how to do a basic BLAST search using a local database It also demonstrates how to perform a multiple alignment using the result of a BLAST search The following operations are examined in this section BLAST search e Obtaining a GenBank file from NCBI e Multiple alignment e Adding annotations to the sequence 7 3 1 Starting DNASIS MAX Refer to Starting DNASIS MAX in 7 2 ORF Search 7 3 2 Using the Editor to Open Sequence Files The Tutorial uses Tutorial2 fsa as its input sequence Select Create a new project from the initial dialog box For Type select DNA and for Content select Sequences from files then click the OK button Specify Tutorial2 fsa from the dialog box that appears For the location of tutorial d
342. the motif 1 Click the Motif Search Amino Acid button from analysis button view and an Analysis dialog box will appear Then click the Parameter button 2 Click the Setting button Amino Acid Motif Database Manager appears 3 Select a motif database to which you want to add motif data 4 Click the View button to display a list of motifs registered with the database 5 Click the New button to display the Amino Acid Motif Property dialog box as shown in the figure Amino Acid Motif Property Motif Name Motif Pattern Pattern Assistant gt Motif Pattern Test Sequence jest Motif Annotation Help Cancel oil 6 Enter the motif name motif pattern and motif annotation optional and then click the OK button 7 The new motif is added to the list 8 To edit motif data select the motif and click the Property button Browsing the Detail of a Motif Searched for If you double click a motif in the Sequence View the details of the motif are displayed 146 Details of Analysis Motit Name ASNGLYOOSYLATION SSS Motif Range E3 ee N Motif Annotation ASN GLYCOSYLATION PATTERN PS00001 APR 1990 CREATED APR 1990 DATA UPDATE APR 1990 INFO UPDATE cosylation site Neel NPI IST P TAXO RANGE 7E7 5 SITE 1 carbohydrate SKIP FLAG TRUE Vi PDOCOO001 ea 1 ASN_GLYCOSYLATION BEGIN Heo N elycosylation site PEARKE It has been
343. the original database where the subject sequence has been registered Length Shows the length of the subject sequence Score Shows the score of a match A match with a higher score value is higher in similarity Expect Shows the expected value of a match A match with a lower score value is higher in similarity Identities Shows the percentage of the matching bases or amino acids within the entire length of a match Positives Shows the number of groups in which the score has a positive value within the entire length of a match when the query sequence and the subject sequence are compared for each amino acid Gaps Shows the total number of gaps inserted into the query sequence and the subject sequence This cell remains blank when there is no gap List View By default sorting is carried out in descending order in terms of Score To switch sort items click the title part each time you click the order alternately changes between descending and ascending Once the sort item is switched through a title click the current sort item becomes the second sort item Explanation of Window Images Item name Description Parameter name No Line number ID Shows the ID of the entry in the original database where the subject sequence has been registered Definition Provides a brief description of sequences Score Shows the score of a matching part Any matching part with a higher score value has higher similarity Evalue
344. thout saving changes to the parameters Chapter 4 Details of Parameters 223 Kind Color Setting dialog Add Edit Delete Import Color Export Color Cancel Item Description Use Kind Color Setting Select to use the specified color setting Kind Shows the type of color settings under Kind Color Displays the type of color Add Adds color settings Edit Edits the selected color setting Delete Deletes the selected color settings Import Color Imports color settings Export Color Exports color settings Set Color Sets colors OK Saves color settings and exits from the Kind Color Setting dialog Cancel Exits from the Kind Color Setting dialog box without saving color settings Annotation List dialog m Annotation List piae ziii Eile Edit Help uj sjej a 2x o alela Comment gene Det8 note DNA a CDS hittp www nebinimnihgo 1 167 1513 Def8 gene gene Def8 note Al449 _http mmww ncbinImnihego 1 3229 0 M source source organism Mus musculus http www ncbinImnihgo 1 3229 0 misc_fea misc_featu note C1 Region Protein 572 724 0 0 misc_fea misc_featu note DAG_PE bind Reei 572 724 ANE IZ Draw annotation name and kind File menu Description Save All As Stores all the annotations as tab delimited text Save Selected As Stores the selected annotations as
345. tiismrmecn qaeriplfwe svlit PKC PHOSPHO SITE Map View A pin shows the retrieved motif If you move the cursor to the pin and click the mouse the display color changes to the selecting color indicating the motif is selected At the same time the sequence in the motif region is also selected Sequence View Together with the sequence this View displays the motif name and the identified part Click the mouse on a motif to select it At the same time the sequence in the motif region is also selected What is displayed within a red frame in the Map View is now displayed in the Sequence View Search Using a Motif Database 1 Click the Motif Search Amino Acid button from analysis button view and an Analysis dialog box will appear Then click the Parameter button 144 Details of Analysis Amino Acid Motif Search Parameterset Editor IV Use Motif Database VIPROSITE Release 13 Check All Uncheck All T Use Input Pattern Help OK Cancel 2 Place a checkmark in the Use Motif Database check box and select an appropriate database from the list of databases displayed To create a new database click the Setting button and use Amino Acid Motif Database Manager 3 Click the OK button to complete the setting Search by Entering a Motif Pattern 1 Click the Motif Search Amino Acid button from analysis button view and an Analysis dialog box will appear Then click the Paramete
346. time to complete DNASIS requires only ten minutes to calculate multiple alignments for 40 data items but it may require two days for 200 data items This applies when the average length for the input DNA sequences is about 1 5Kbp Longer sequences such as a gene or a complete genome require a longer time If you have many known sequences and want to calculate alignment between an unknown sequence and the known ones you can save the time required to calculate alignment with the unknown sequence by creating a profile alignment of the known sequences first Calculating a profile requires the same time as a typical multiple alignment However once a profile is created DNASIS can calculate alignment with the unknown sequence much faster in about 10 seconds for the above example Disadvantages of using a profile Using a profile provides fast calculation However it results in degraded alignment precision The same set of sequences may produce different results when you use a profile and do not use a profile You should consider the above mentioned caveats when using a profile Procedure for Creating a Profile As for any other analysis click the Analysis menu and the tab DNA Multiple Sequence Note that this option is available only when in Sequence mode 1 Enter or import sequences you want to align in order to create a profile into the Main window 2 Click the Make Multiple Alignment Profile button and an Analysis dialog box ope
347. tion provides homology search using the BLAST search service from the NCBI Web site For the analysis establish an Internet environment Types of BLAST Search There are three types of BLAST search for DNA sequences Button name Program name Description BLAST search blastn Homology search between DNA sequences and a DNA sequence database BLAST search blastx When you enter a DNA sequence performs an all frame translation and then Protein DB a homology search between amino acid sequences and an amino acid sequence database BLAST search tblastx When you enter a DNA sequence performs an all frame translation and then Translation DB a homology search between amino acid sequences and the DNA sequence database that has been translated for all frames Explanation of the Result Window Refer to 3 19 BLAST Search Selecting a Database to Be Searched 1 Click the BLAST Search icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and the Internet BLAST Search Parameterset window will appear 2 Click Setting to display the NCBI Advanced BLAST Search window NCBI Advanced BLAST Search NT Program blastn v Database rv Se Database for DNA sequence search AA Program blasto Database fre x Option Word sive for nucleotide 11 J amp Expect lt 10 I Perio Database for amino acid sequence search Filter I Low complexity M Huma Descri
348. tiple Alignment Profiles Phylogenic Tree Using Profiles Sequence Assemble Amino Acid Basic Amino Acid Content Isoelectric Points Hydrophilicity Hydrophobicity and Secondary Structure Amino Acid Search Motif Search Common Motif Search Proteolytic Site Search Amino Acid BLAST Search Comparison BLAST Search Translation DB One to One BLAST Search Internet BLAST Search Internet BLAST Search Translation DB Smith Waterman Search One to One Smith Waterman Search Amino Acid Multiple Alignment Multiple Sequence Phylogenic Tree Chapter 3 Details of Analysis 67 Creating Multiple Alignment Profiles Phylogenic Tree Using Profiles NCBI Entrez Search 68 Details of Analysis 3 2 Complement Sequence This function converts DNA sequences into complement sequences and then adds them as new sequences Explanation of the Result Window De WH mamme Der tp x DSA ASB SAABS Le Aan SAB S s vo e gt BSS DG wis ONA Bane Map View Sequence View sequence tracewet C oe ACA Complement Sequence Sequence View The complement sequence is displayed below the specified sequence The sequence name consists of the original sequence name followed by _C Example If the sequence to be analyzed is ACTTGAGAT clicking the Complement Sequence button converts it to TGAACTCTA Chapte
349. to be displayed Emphasis match part in multiple sequence Perfect match Match more than Match less than Sets the background color and character color when displaying alignments Sets the color of the background for a position with a perfect match Sets the color of the background for a position whose hit rate is greater than a specified value Sets the color of the background for a position whose hit rate is less than a specified value Colorize Sequence When checked alignments are displayed in color When not checked alignments are displayed in black Background Sets the background color for each character Specify different colors for DNA and amino acids foreground Sets the color for each character Specify different colors for DNA and amino acids Initialize Initializes all settings to factory presets Use Defaults Stores the settings Folding Ruler Tab x Fort Sequence FoliegFute Fold Sequence T Show Pibe No Fokting Line bbp ee Fok ty wero wath apes Foii ever fi bp ss ire r Show paion OF evey sequence Block Lengel boss beska d Use a Detaas ee Item Fold Sequence Description Sets how to display sequences in the Sequence View No Folding Uses one line for displaying a sequence Fold by window width Displays a sequence by folding it back according to the width of the window A change in the window size will automatically change the fold back width a
350. to the motif data and closes the Nucleic Acid Motif Database dialog box Help button Displays online help Editing the Properties of a Motif You can view and edit the properties of a DNA motif registered in the database 1 In the analysis button view click the DNA motif database The Nucleic Acid Motif Database Manager appears 2 Select the database containing the motif you want to display and click the View button The Nucleic Acid Motif Database dialog box appears 3 Select the motif you want to edit from the list and click the Property button The Nucleic Acid Motif Property dialog box appears as shown in the figure Make the necessary settings After completing editing the properties click the OK button The following describes details about the dialog box Nucleic Acid Motif Property Motif Name Motif Pattern EBTAATCYY Pattern Assistt i a Motif Pattern Test Sequence Est Motif Annotation SS eS Item Description Motif Name Name of the motif You cannot edit this item if the database is locked The motif name must not exceed 255 characters Motif Pattern Pattern of the motif You cannot edit this item if the database is locked Pattern Assistant Beginning of the sequence Any character End of sequence Or Grouping Character Class Character not in the list Match 0 or more times Match 1 or more times Match 0 or 1 times Match exactly n times
351. tton converts it to TAGAGTTCA Chapter 3 Refer to 5 8 Codon Table Details of Analysis 71 3 5 Translation This function translates DNA sequences into amid acid Explanation of the Result Window osu bee aR tBF 1 248 zs 232 Da was Bar for displaying a translation Map View Sequence View Result of EEA Map View In the color display mode this view displays a bar that shows the sequence in the colors of amino acid residues By default the property of amino acid is classified into four groups acidic basic neutral polar and neutral nonpolar The color for each group is set as follows pea pone feon Bue feas fs wo m Yellowish green Neutral Polar Trp Ser Thr Cys Gin Asn Tyr Green Neutral Nonpolar jAla Val Leu lle Pro Phe Met Gly Sequence View This view displays the translated amino acid sequences in a three row pattern for each frame The sequences are translated according to the conversion rules in the Codon Table The DNA sequences are translated for each group of three characters so that some bases may not be translated Order of translation gt GTC GCC AAG CAC AT V A K H Not translated This function translates a nucleic acid character string that differs from any of the combinations specified in the Codon Table as follows 72 Details of Analysis 1 Any replaceable characters are replaced The Codon Table is searched for all com
352. u iia rainane aa raain aaa ane aaa Earra er raaa aa araa aia aa aaar taa 252 Editing a Codon Table ranno oieee KAEA ENEA KAS RAE RANA Su oseawnidesauaetn otoueuvosasneuvenesvonsotls 252 5 9 DNA Motif Database cece sce vinina eeseeeeesneeseseassneessaneesssneessaesesneesaaneessseevsseesaanoensenens 253 WAnGOw DeScrip t1Om 3252 25 55 32 ssad sessed AET ET AE T EE E E E Editing the Properties of a Motif Database cccescescessceceeseeseeseesecseeeeceaeeaeeaeeaeceeeeaeeaecaecaeeeeeeaeeaeeneens Displaying a List of Registered DNA Motifs a Editing the Properes ofa Motif iee era capaanccsesvencceapavacettoveuss EE EEE EEEE 5 10 Proteolytic Enzyme Database ssssussesnunsennnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnna 257 Window Description e aa Nae pide E a SE E E E NEA rave tout R E A 257 Creating New Proteolytic Enzyme Data i oiiire citna resi eir eniai o EE REEE AAEN RAE 257 Editing Proteolytic Enzyme Data Importing Proteolytic Enzyme Data K Exporting Proteolytic En yme Data iciscccccicisscessiscerscasdceaesaistessecsicesessascascessacereadavesascvieiseassavesacssieaccssane 5 11 BLAST Search Dedicated Database 0 cccccecssssseeesneeseseeeseneaesneesesneeseseeeseeasenneesennens 262 Window Gescrip ti Onis lt sraa pai AEE e EEE e EE AA AR deavesecdseve 262 Chapter 6 Create Plasmid Maps ccccccceeeeeeeeeeeeeeeeeeeeeeeeeaeeeeeeeeeeeseeeeeneeeeseeees LOA 6 1 About Creating P
353. uence and then Reverse Complement or clicking the E button on the toolbar Conversion into the reverse sequences of complement sequences The entire of a sequence being edited undergoes the process of conversion Returning to the Pre Edit Original Sequences This process is intended to cancel all changes made on a sequence being edited so that the sequence will be returned to the original state immediately after it was read from a file 1 Select Sequence and then Revert 2 In the confirmation box click the OK button Chapter 2 DNASIS Basics 43 2 8 Analyzing Sequences advanced Refer to Changing Analysis Names in 2 8 Analyzing Sequences advanced Displaying Results of Analysis Side by Side The results of analysis from different analysis buttons are automatically displayed in a vertical format Usually the result of analysis of the same type is overwritten However you may want to avoid overwriting during such analysis for example when you have changed parameters or edited sequences In that case proceed as follows 1 Perform the first analysis 2 Perform operations such as changing parameters or editing sequences 3 Repeat analysis 4 In response to a message saying that The analysis xxx of sequence xxxxx already exist What do you want to do click the Add button 5 Preferably you should change the analysis name 6 Repeat steps 2 to 5 as necessary ioe Spss tet iriea
354. uence database folder specified in the parameters and obtain a database list from that folder Item Database List F barok o maze of MK bisnise a 10A OP A HIK Ier NA o wAe P Howen MA a ao p um D DONAA eha mannalun sequences 4 Description Shows a sequence database list The databases listed are only for sequence types DNA or amino acid that were specified in the prompt dialog Database Icon Database Name Entries Update Database Comment Shows the database icon Shows the database name Shows the number of entries Shows the date of update Shows comments regarding the database Open button Click the button to start a Select Entry dialog Shows the database entry selected from the database list DB Path button Click the button to start a database path dialog Specify the sequence database folder to reference Close button Click the button to close the dialog Showing Entries To start click the Entry View button from the Select Sequence Database dialog Select tntry a Search Field IR Search Key toys 1 PBB gt 1D e mm ms Databaze Source DIMISE AALMTOYTOB Detinition Item Search Field ices akes americans cytochrome b gene partial ods mitochondrial gene for jeitochondial product 324 of BPs par AG TTCOGT TOTOTATTAGGAGTTTGGTTARTCT TADAARTOCTTACAGGAG Un re Tena Tea ore ae eT PATTOTOOTOT TTOGATA
355. uence iv DNA AFO54247 Sequence Vv DNA AF054248 Sequence Vv DNA AFO54249 Sequence M DNA AF054250 Sequence Vv DNA AFO64490 Sequence Vv DNA AF139594 Sequence Vv DNA AF165045 Sequence Vv DNA AF165046 Sequence Vv DNA AF165047 Sequence Vv DNA AF165048 Sequence Vv DNA AF165049 Sequence Vv DNA AF165050 Sequence Vv DNA AF165051 Sequence Vv 2 Uncheck the Seq field of the sequences you do not want to add 3 Click the OK button 4 Click the Multiple Alignment button to start analysis Perform an analysis after canceling the alignment display mode Alignment after Masking Regions within Sequences 1 Select region within one or more sequences and press the IN button on the toolbar The selected region is shown by an N and masked as shown in the figure and is not considered in calculating the alignment 10 20 30 40 50 Sequence NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN Neccaccce ctga Sequence NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNN Sequence NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNN gccccct Sequence NNNNNNNNNN NNNNNNNNNN t Sequence Sequence Sequence Sequence Sequence Sequence Sequence Sequence Sequence Sequence Sequence Sequence 2 Click the Multiple Alignment button to start the analysis 3 The analysis will be performed without including the masked part as shown in the figure 20 30 0 50 Sequence NNNNNNNNNN NNNNNNNNNN NNN NNNNRINNNNG D0AGDOODC Sequence NN
356. upported Default button Returns parameters to default values Primer Picking Conditions xj Penalty Weights for Primer General Parameters Primer Soe Mn Primer Tm Mn Max Te Oviterence Product Ta Me Primer GOR Mn Max Sell Compienenta ty Max Ss hide Taget Penalty Fret Base hide Set Concentration D Ubers Base Hyb Olieo Conditions Penalty Weights for Hyb Oligo Primer Picking Condi ions Pre Sequence Inputs Op Bo Max F E7 O Fo ME Opt Ma a Opt Max aor Outside Target Penalty D Ma F Set Complementarity Max Poly X E OO Clamp f Areeaine Oleo Concentration fF Item Primer Size Description Specifies the minimum value Min optimum value Opt and maximum value Max for the length of the primer sequence bp DNASIS MAX will not select primers shorter than the minimum value or longer than the maximum value It will select a primer having the size closest to the optimum value You cannot set the minimum value to 1 or less or the maximum value to greater than 36 The maximum value of 36 is a limit due to the maximum sequence length when calculating the Tm value The minimum value cannot exceed the maximum value Primer Tm Specifies the minimum value Min optimum value Opt and maximum value Max for the primer Tm value Celsius DNASIS MAX will not select primers having Tm lower than the minimum value or higher than the maximum value It will select a primer h
357. ur example of the Tutorial we can see mutations at the 59bp and 74bp locations Index A ABI Format 26 ALF Format 26 Amino Acid Content 138 220 Analysis 67 Analysis Button 4 Annotation 53 224 Annotation List 225 Annotation Setting 224 B Base Content 76 Blast Search 110 114 135 157 158 201 202 218 264 294 Bootstrap Tree 124 163 C Clustering 132 217 Codon Table 254 Codon Usage 77 181 Color 39 60 74 118 Comment 29 Comment View 3 Common Motif Search 149 Complement Sequence 69 176 Consensus 120 160 Copy 64 D Data List 15 Databases 228 Database 232 Duplicate 262 E Edit 46 126 269 288 Editing Sequence 30 41 EMBL Format 26 Exit 284 F File Format 24 Font 38 123 162 G GC Content 79 182 H Hairpin Loop Search 198 Hydrophilicity 143 222 Image 64 In house 232 Inline view 33 Insertion Pointer 30 Internet Blast Search 114 158 202 Internet Settings 286 Internet Settings 13 Index 301 Isoelectric Point 141 221 Isometric point 141 J Jump 51 K Kind Color Setting 225 Main Window 2 Map View 3 Mask 41 119 301 Menu Bar 8 Motif 99 145 149 196 241 255 292 Multiple Alignment 117 127 160 164 204 210 252 296 Mutation 102 197 N NCBI Entrez Search 166 169 O Oligo Probe 193 Oligo Probe Design 93 One letter 290 ORF 85 185 288 ORF Search Result List 18
358. ust specify a primer sequence in the direction of 5 to 3 on the input sequence pick right primer Specifies whether to design a right primer 3 downstream primer To design the right primer select the leftmost check box You can also directly enter a sequence to specify the primer You must specify a primer sequence in the direction of 5 to 3 on the complement sequence of the input sequence pick hybridization probe Specifies whether to design a hybridization probe for an amplification segment with a designed primer To design the hybridization probe select the leftmost check box You can also directly enter a sequence to specify the probe You must specify a probe sequence in the direction of 5 to 3 on the input sequence Sequence ID Not supported by DNASIS MAX Target Specifies a region or regions you want to have the PCR reaction product contain Enter regions as follows startbp length startbp length startbp length Example 1 Specifying 50 2 indicates that the product will contain 2bp from a position SObp away from the 5 end that is bases 50 5 lbp Example 2 Specifying 50 2 80 5 indicates that the product will contain 2bp from a position 50bp away from the 5 end and 5bp from a position 80bp away from the 5 end that is bases 50 51 bp and 80 84bp To specify more than one region delimit regions with a space When more than one region is specified DNASIS MAX will design a primer which cont
359. utton Displays the search parameter input window for narrow down search while keeping the current search conditions The search results are stored The stored results can be retrieved from the next data list window Chapter 3 Details of Analysis 167 3 44 Searches Using Genelndex Use GenelIndex to perform Homology Search as well as Motif and Domain Search Performing a search requires an internet connection For operating environment details refer to GeneIndex 2 2 Operation Manual Obtaining Accounts The search engine that GeneIndex uses requires two accounts A DNASIS account that is included in the DNASIS MAX package and a Genelndex contract account The DNASIS account and password are located inside the DNASIS MAX package If you do not find it inside the package please contact our support center Also if you are making a new Genelndex contract before using the function for the first time you must first log in to the account from the website http index dnasis jp agree to the contract terms and change the default password The number of users that can log in at the same time will depend on the contract options of your GeneIndex account If you try to log in when number of users has already reached a maximum an error message will appear When you leave the website be sure to log out Set Genelndex Server Information Before performing a search you need to set login information for GeneIndex Server The login setting you m
360. vcceccsssscesccsseucsasaveascsnsvvacecansenccsnseva ce EEE avsvedesnevwacs cavsvadesseveactsevsvuteieess 82 Trimming Unconditional Bid asyano E EEEE REEE 82 Analyzing the Trimmed Sequence sica E R duusssuedasoneceensbeeneceosae 82 HES E ee E E E E 84 Explanation of the Result Window 84 Changing the Codon Table 84 Changing the Start Codon i ois ra E EA ERNE AER E ERAR E 85 Listing the Res lt of a Seatch for ORES rreo ee air E EA ORE E Ros eae EAEN 85 Selecting AMORF to Display ii nnas eE ERE EE A ER ERER 85 Narrowing Down the ORFs to Display crsssseunieenieinnncnicannneanaaa nna 85 Adding a Selected ORF Sequence to the Editor eee cceceseceeeeeeseseescsesaceecseeseesseeesseescsesseeeeseeaes 86 Adding a Commentto a Selected ORF sccse sssecsce nna a R E 86 Creating Amino Acid Translated Sequence for an ORF eccecececeeescesesececeeeseeeeseeseseeseeecaeeecetseeeeseeeee 87 3 11 Primer Desig iarna anran nana EN eaan ENANA ENTARA EEEN ENAREN NEENAKE ARENAN 88 Explanation of the Result Window cccccscsssssssssssseeeesececeeceecesecsecsecseceeeaeesecseseesseeeeseaeesecaeeeeneseneeaees 88 Displaying the Primer Listy Mind eatin e EE RAEE RT EE sone ien hunger 88 Selecting the Primer That Amplifies a Selected Range wo ieee eseeeeseeseseeseeecseescseeecsesseesseeesseeaeees 88 Selecting a Primer to Display rea lec secon na EE thes coves cess purses EE E E EREE RE aS 89 Changing the Tm Value for a Primer to be Designed
361. videnced by a copy of your receipt that 1 The Software unless modified by you will perform the function described in the documentation provided by Mirai Your sole remedy under the warranty is that Mirai will undertake to correct within a reasonable period of time any marked Software Error failure of the Software to perform the functions described in the documentation Mirai does not warrant that the Software will meet your requirements that operation of the Software will be uninterrupted or error free or that all Software Errors will be corrected 2 The media on which the Software is furnished will be free from defects in materials and workmanship under normal use Mirai will at its option replace or refund the purchase price of the media at no charge to you provided you return the faulty media with proof of purchase to Mirai Mirai will not have any responsibility to replace or refund the purchase price of the media damaged by accident abuse or misapplication THE ABOVE WARRANTIES ARE EXCLUSIVE AND IN LIEU OF ALL OTHER WARRANTIES WHETHER EXPRESS OR IMPLIED INCLUDING THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY MIRAI ITS EMPLOYEES DISTRIBUTORS OR AGENTS SHALL INCREASE THE SCOPE OF THE ABOVE WARRANTIES OR CREATE ANY NEW WARRANTIES SOME STATES DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU IN THAT EVENT
362. vsiucasceseicchausiecasessuacahaseideaussayioey abe ievaussesacsestetiesectt 290 7 3 BLAST Search 292 7 32 Starting DNASIS MAX senansa oee T soaesie3 sees subs AE E T da medsviesuedsde a sesedusasestte 292 7 3 2 Using the Editor to Open Sequence Files 292 7 3 3 Specifying the Database as the Target of BLAST Search 292 734 Running BLAST Search lt sched ass cecsthss sacl ugd neste seneuhecsets a e a E autehcessberNiesaevdes oteuveuss AE ES 293 7 3 5 Using the Editor to Enter the Highest Homology Sequence as a New Sequence from the Search Result Window 293 7 3 6 Running Multiple Alignment 3 5 ccisceissecsesssecgseeizeessuassncsseia chegsaeasncdsdec sacs SEn AE EEE SEE Ee S ERSA AEE Sk EEE SSS EEES SRNE SISE 294 13 1 Adding Annotations to Similarities i oee asesi o ENEE EESE VEEN EEE ENEE ENEE ENE EE S EEEREN EEEn 294 7A VOCtor TAMMA eaaa eaaa eN AA cc deen S EUAN AAA ANANN ceuestagessetadeerenaseeseani covers 297 14 1 Starting DNASIS MAX ooreo naaa ia N TUN A ONEA OEV T N E AENEAN 297 7 42 Using the Editor to Open Sequence Piles sz ssiss c iscsevssscccessadscdavs e EEVEE R ERROS 297 7 4 3 Registering Vector Sequences with the Vector Database s ssesssesessssesessssssstsssrsrsrsrsrstsrstntsrnrssnesstsrntnterntererererenerereret 297 TAA Carrying Out Vector Trimming cessed vec teens tes REEE EE Eaua EEEE ENAA AASS EAE EAEE EEA EEEE 298 TAS Masking Vector SCQUENCES seye eE e A AE E EEE ES E E AS 299 TAG Switchingto
363. ween 16 and 0 inclusive and must not be smaller than the setting of Initial Gap Max Num of Return Specifies the maximum number of results you want to obtain Specify an integer between and 500 inclusive Cut Off Score If you select this check box DNASIS will only output hits having a score larger than the specified score If you do not select this check box DNASIS MAX will output hits regardless of the score Target Database Specifies the databases to be searched The list box displays database name Select the check boxes of the databases you want to search Default button Returns parameters to default values 202 Details of Parameters 4 21 Multiple Alignment DNA and Amino Acid General MultipleAlgnmentParametertdtor xj GeneralSettings PairmiseAlienmers MultipleAlienmert ProisinGsp Tree Seqwnnee Type ommaan Quiput Order Order by Alianed F Use FAST Alecrithm for the slianment Protein Chere ABCOEFGHK MNPORS TUVWxY2 DNA Chars ABS DGHKMNESTUVWY Select create datas C Do Matole Alerment and Tree Do Multole Alert only C Do Tree only Parameter Sequence Type ret mo Description DNA or Protein is automatically selected depending on the type of the selected profile Note Clustal W can process both DNA sequence data and amino acid sequence data This parameter causes Clustal W to handle the input sequence data assuming it to be either a DNA or
364. wnload completes and an installer will start up DNASIS MAX and import the search result file If you click Save from the dialog that normally appears and a file with extension name dnasislzh will be saved to the folder you select Below is the method to import a search result file into DNASIS MAX a Double click on the search result file b Drag and drop the search result file on the DNASIS MAX icon on your desktop c Unzip the search result file with software that uses the UNLHA32 DLL then import the unzipped file 172 Details of Analysis Parameter Set List and Parameter Meanings ir Gene bidey Param Editor x Loen Settre Genelndex Server Leen PADI Password pme Geneindex Contract Account DNASIS Account Contract ID AADO Passord peee Genelndex Account Select Species Human Homo sapers Species Item Description Server Set GeneIndex Server name Port Set the port number of GeneIndex Server DNASIS MAX Account Login IDSet the DNASIS account ID DNASIS MAX Account Set the DNASIS account password Password GenelIndex Contract Account Set GeneIndex user name Contract ID GeneIndex Contract Account Set GeneIndex password Password Select Species Set the species It is possible to select Human Mouse and Rat It is possible to select one from the list The Update button renews the species list About Genelndex 2 2 For details on how to use refer to Ge
365. wo ways of specifying the motifs to be searched for one using a database and the other by keying in any sequence pattern Explanation of the Result Window Map View Sequence View Target Utegi Seticted O21 to Map View The pin shows the found motif If you move the cursor to the pin and click it the display color changes and the pin goes into the selected status Sequence View Together with the sequence the following are displayed the name of the motif and the part of recognition If you click the motif name it is displayed in the predefined color and the sequence that contains the motif also goes into the selected status Searching for Motifs listed in a Database 1 Click the Motif Search icon in DNA Search from analysis button view and an Analysis dialog box will appear Click the Parameter button and the Nucleic Acid Motif Search Parameter Set Editor window appears 2 Place a checkmark for the Use Motif Database and select the database displayed in the list ch Parameter Set Editor as 3 VISAMPLE Check All Uncheck All Setting 3 Select the OK button Searching for a specific sequence Motif 1 Click the Motif Search icon from analysis button view and an Analysis dialog box will appear Click the Parameter button and the Nucleic Acid Motif Search Parameter Set Editor window appears Chapter 3 Details of Analysis 99 2 Place a checkmark for the Use Input Patter
366. xpott Description Outputs the entire data into a text file Note that you Print Preview Displays a print preview Print Setup Makes a printer setting Print Starts printing Exit Closes the window Edit menu Description Undo Cancels the previous operation Cut Cuts the data Copy Copies the data Paste Pastes the data Select All Selects everything Find Attempts to find the target Find Again Attempts to find the next target View menu Description Navigation Toolbar Toggles the Navigation toolbar to display or hide it Format Toolbar Toggles the Format toolbar to display or hide it Status Bar Toggles the status bar to display or hide it Help menu Description Contents Displays online help About GridViewer Displays the version information about Grid Viewer Setting the Clustering Standard 1 Click the Clustering button from analysis button view and an Analysis dialog box will appear Parameter button and a Sequence Clustering Parameterset Editor will appear Sequence Clustering Parameterset Editor Sequence Type Nucleotides C AminoAcid Clustering Mode Clustering only input sequences each other C Clustering with existing cluster DB Breh SOtst CSs Ci CS s i Clustering Conditions Score is more than 200 and overlapping length for query length is more than mo OK Cancel
367. xternal definition file for the keyword REFERENCE You can define more than one REFERENCE Files you can import File format You can import files complying with the GenBank format How to import a file Search a file that complies with the GenBank format for primary search keys If the key is found in the file the value defined with that key will be imported You must define primary search keys in the order in which they are shown in the following table Primary search Secondary search Description key key LOCUS Searches for the string Circular and if found recognizes the item as Circular DEFINITION Imports a string excluding the string DEFINITION itself as the definition ACCESSION Imports a string excluding the string ACCESSION itself as the accession REFERENCE Regards the string REFERENCE as the start of a reference Until DNASIS finds a next REFERENCE or finds a FEATURES it searches for AUTHORS TITLE JOURNAL and MEDLINE as the definitions for a single REFERENCE item Chapter 5 Refer to Defining Start and End in Importing a Sequence from an External Definition File of 5 4 Vector Database Databases 237 Primary search Secondary search Description key key AUTHORS Imports a string excluding the string AUTHORS itself as the authors TITLE Imports a string excluding the string TITLE itself as the title JOURNAL Imports a string excluding the string JO
368. y You can edit the comments if the database is not locked OK button Saves the changes made to the properties and closes the Amino Acid Motif Database Property dialog box The changes are canceled if a database having the same name is already registered Cancel button Discards the changes made to the properties and closes the Amino Acid Motif Database Property dialog box Displaying a List of Registered Amino Acid Motifs You can display a list of all motifs registered in the amino acid motif database In the Amino Acid Motif Database Manager select the motif database for which you want to display a list and click the View button cid Motif Datat Database Name PROSITE Release 13 118 SEED STORAGE 1433 1 1433 2 258 SYNTH1 25A SYNTH2 2FE2S FERREDOXIN 3 HYDROXYISOBUT_ 3HCDH 43 KD_POSTSYNAPT 4 DISULFIDE CORE 4FE4S_FERREDOXIN 5 NUCLEOTIDASE 1 5 NUCLEOTIDASE 2 6PGD A4_EXTRA A INTRA A DFAMINASF NG DE RNLIL H2ILIVMF ISVIGATYKN YK DE STLIMQLL R FYI ial LIVM D 2 GAJINO GATIE KRITLIEK DEJPT GAITO IGLG MG PM F LIVMF QI 2 0 6 06 ASIG PEG LIVMHHHE LIVMIGNHE Fy VCCP GYENPTYIKR SILTYMIINSITDDP 11S_SEED_STORAGE PATTE 1433 1 PATTERN nAG PSOL 1433_2 PATTERN nAG PSOC 254_SYNTH1 PATTERN nAC 254 SYNTH_2 PATTERN nAC 2FE2S_FERREDOXIN PATTER 3_HYDROXYISOBUT_DH PATT 3HCDH PATTERN nAC PSO 43_KD_POSTSYNAPTIC PATTE 4 DISULFIDE CORE PATTERN
369. ysis currently displayed in the Sequence View Using A and Q on the toolbar allows you to expand and shrink images About the Target in 2 9 Editing and Analyzing Multiple 1 Indicates the sequence name The sequence specified as the target in the Sequence View is underlined 2 Indicates the analysis name The sequence specified as the target in the Sequence View is underlined y q p 8 q Sequences 3 Displays the red framed area in the Sequence View 4 Displays the ruler Comment View Pane OCUS AAKS 7570 219 aa INY 03 SEP 2001 a EFINITION cytochrome c oxidase subunit I Tremoctopus violaceus CCESSION AAK97570 ID 215421850 ERSION AAK97570 1 GI 15421850 BSOURCE locus AF377978 accession AF377978 1 OURCE Tremoctopus violaceus ORGANISM Mitochondrion Tremoctopus violaceus Eukaryota Metazoa Mollusca Cephalopoda Coleoidea Octopoda X 5 The Comment View Pane displays a comment when you read a comment based file in any of the FASTA GenBank Flat EMBL PIR and former DNASIS formats You can toggle view and hide a comment by clicking the button ES on the View Toolbar You can edit the comment directly If several sequences have been read and displayed the comment activated is the one belonging to sequence active in the Sequence View Pane Window Descriptions Analysis Button View Pane The Analysis Button View Pane displays and gives you access to the analysis
370. ze Corresponds to the ktuple parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter specifies the size of a completely matched sequence A larger value results in faster calculation A smaller value results in higher precision No of top diagonals Corresponds to the topdiags parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note Clustal W calculates the number of complete matches within each diagonal matched position in the sequence and uses the matches having high match ratios for alignment This parameter determines the number n of completely matched positions to be used the n highest match ratios will be used A smaller value results in higher precision A larger value results in higher speed Window size Corresponds to the window parameter of Clustal W Either the value for amino acid or that for nucleic acid is used depending on the Sequence Type setting Note This parameter specifies the number of diagonals around the completely matched portion that are used for alignment A smaller value results in higher precision A larger value results in higher speed 204 Details of Parameters Multiple Alignment MultipleAlignmentParanmeteriditor Fi xj GeneralSettings PaimiseAlienmera MultipleAlianment Proseintap Tree Gap Qen Penalty 00

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