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1. 46 RECOG Client User s Manual Cluster dist The cluster distance and sub cluster distance are displayed Phylogenetic Pattern Coefficient In a similar phylogenetic pattern search the coefficient of correlation with a specified pattern is displayed 11 3 Display Nondisplay of the homology cluster header 1 Click the right mouse button on the cluster header click the menu and click Show Hide homology cluster label 11 4 Species color setting The species color is set The color set here is reflected in the background color of the PPM species header and the locus tag label of the phylogenetic tree in the multiple alignment analysis 1 Select the species on the Taxonomy Tree at the upper part of the Selected tab click the right mouse button and click Color organism Choose in the pop up menu The Color palette screen is displayed 2 Set the color on the Color palette screen and click the OK button to set the species color 11 5 Changing the PPM cell boundary color 1 Select Color Base Color on the control panel click the right mouse button and click Edit to display the PPM tab on the Option screen Taxonomy Tree PPM Function Category Color Neighboring Cluster Multiple Alignment Tree General V Background color for cells containing inparalogs gt 2 gene ID V Display gene names or the number of genes Z cole tor border ines Background color for ingroup cets
2. result 39 RECOG Client User s Manual 9 4 Display of the DomClust analysis result properties For the DomClust analysis result the parameters for the DomClust execution the applied PPM sorting conditions etc are displayed Also the RECOG server can be edited for default access by the currently displayed DomClust analysis result 9 Click Option Properties to display the Properties screen Ed Properties ject le name Cluster Tab ID Nurriber of Select Genomes hgroup organisms Outgroup organisms Muriber of Phylogenetic Patterns Murnber of Clusters Organism Filter Fitter by minimum number of organisms DormeClust Options Cutoff BLAST E value Cutoff DP score Alignment coverage for domain spitting Score cutoff for domain splitting Similarity measure for orfhology Best hit criterion 10 To edit the RECOG server select the server from among those listed by double clicking value in the Server drop down menu and click the Apply button 40 RECOG Client User s Manual 9 5 Storage of the DomClust analysis results The DomClust analysis result is automatically saved to the project directory or one of its lower level directories when the analysis is conducted To refer to the analysis result using another tool save the analysis result in DomClust format dclst or tab delimited format Although the tab delimited format file is useful for loading it into and displaying it on Excel et
3. 1 The ortholog analysis is performed and the results are displayed as described in 9 2 Execution of DomClust and 9 3 Display of the DomClust analysis results 2 Click 89 gt Core genome alignment CoreAligner in the Toolbox The Core Genome Alignment screen is displayed 3 Specify the conditions for the analysis carried out by the CoreAligner program on the Core Genome Alignment screen There are two ways of specifying the analysis conditions Simple Mode and Expert Mode Simple Mode Expert Mode Assignable Reference genome Reference genome item Cutoff ratio of conserved orthologs Cutoff ratio of conserved orthologs and neighborhood relations Cutoff ratio of conserved Window size neighborhood relations Use unuse species group Window size Use unuse species group Display Nondisplay of species Display order of species Simple Mode Gore Genome Alienment Reference Genome Window Size Use sp group RECOG Client User s Manual Expert Mode Gore Genome Alienment B orvyiotquetaciens FZB42 B aenyloliquefaciens F ZB42 Bsenyioiquetacions FZB42 B eevyloliquelaciens F ZB42 B aeryloiquelaciens FZB42 B cevyioiquetaciens FZB42 MO00000 C folt ratio of conserved genes WY Citolt ralio of conserved cormections 6 Required coverage of each genome for each chister Citolt of deletion score for removing local regions Other Options F Use sp g
4. H Desulfurococcales 4 J oy Desulfurococcales 4 i H Desulfurococcaceae 3 gt Desulfurococcaceae 3 ameropyrum pernix K1 LeAeropyrum pernix K1 Lionicoccus hospitalis KINGA L staphylothermus marinus F1 Lionicoccus hospitalis KINGA La staphylothermus marinus F1 2 Aee eD LEHyperthermus butylicus DSM 5456 LH perthermus butylicus DSM 5456 mo nana ana i eas n Supplement Rank item modifications To modify the Rank items in the drop down menu 1 Click Ve Option in the Toolbox to display the Option screen 2 On the Option screen click the Taxonomy Tree tab 3 In the Rank Item form on the Taxonomy Tree tab check the taxonomic rank to be 34 RECOG Client User s Manual displayed 4 Click the Apply button on the Option screen 35 RECOG Client User s Manual 9 Ortholog Clustering DomClust Ortholog clustering is performed upon specifying a species The result is displayed on the PPM This is the first analysis conducted in RECOG and is the basis for all comparative analyses 9 1 New analysis If any DomClust analysis result is displayed clear the result 1 Click New New Analysis to clear the currently displayed DomClust analysis result 9 2 Execution of DomClust Note DomClust analysis is possible only in an environment where Internet connection is available 2 Specify the ingroup outgroup by means of the method shown in 8 3 Spec ification of the ingroup o
5. group can be executed Cluster ID The cluster ID is displayed Gene Name The representative gene name of the cluster sub cluster is displayed Description The representative description of the cluster sub cluster is displayed As the background color the color corresponding to the typical function category of the cluster sub cluster is used Gene information table center table The information on the genes belonging to the cluster selected on the PPM or the cluster information table is displayed Upon double clicking a web browser is activated and the details of the gene information are displayed If multiple genes on the table are selected and right clicked various functions including Multiple Alignment and the display of a Regional Genome Map for the selected gene group can be executed Organism The species code is displayed Locus Tag The locus tag of a gene domain is displayed For the domain the domain number is shown at the word s end Detailed gene information table lower table Detailed information on the gene selected on the PPM or the cluster information table is displayed The registered gene properties are also displayed Organism The species code is displayed Locus Tag Locus Tag Gene Name Gene name Accession P Accession number Position Gene region Direction Direction of gene Feature Key Feature key GI number GI number Gene ID Gene ID Description Description 22 RECOG Client
6. to select the relevant species on the Taxonomy Tree on the All tab Selected tab 52 RECOG Client User s Manual 12 Color Display by Properties Each cell on the PPM can be colored and displayed using the gene properties registered as described in 29 1 Registration of gene properties the correlation coefficient determined based on the similar phylogenetic pattern search function etc ILL Color display setting by properties Click Color genes by properties in the Toolbox to display the Color genes by properties screen Specify the coloring conditions on the Color genes by properties screen Organism Specify a species Property Specify properties Value type or enumeration type properties can be colored and displayed Color Set the color on the PPM If the properties are of the value type lt gt Threshold setting The color as per a specified property value is set labels 1 and 2 in the above figure Click the Add color button to set up to four values and colors The color s between them is determined by the linear interpolation method Click the Remove color button to remove the intermediate values Color by Specify whether to set the color based on value Value or ranking Rank The method for assigning rank If the color is set as per ranking specify whether to rank all the species specified All species or each species Every species Automatic update
7. 10 RECOG Client User s Manual 3 Installation Uninstallation 3 1 Installation of RECOG for Windows 1 Set JAVA HOME an environmental variable as follows Variable JAVA HOME Value the directory in which the JAVA JRE 1s installed 2 Double click recog client lt version gt exe to start the installation Install RECOG by following the instructions on the screen Upon completion of the installation process the RECOG menu is added to the start menu 3 2 Installation of RECOG for Mac 1 Double click recog client pkg tgz to create recog client pkg 2 Double click recog client pkg to start the installation Install RECOG by following the instructions on the screen During the installation the administrator s username and password are requested 3 3 Installation of RECOG for Linux 1 Set JAVA HOME an environmental variable with the following command bash export JAVA _HOME lt JAVA JRE home directory gt csh setenv JAVA_HOME lt JAVA JRE home directory gt 2 Decompress recog client lt version gt tgz to create a recog directory Create the recog directory in an appropriate place 11 RECOG Client User s Manual 3 4 Uninstallation of RECOG for Windows 1 Click Uninstall RECOG in the start menu to remove the installation directory 2 Ifthe installation directory is not removed remove it manually 3 The data directory C Documents and Settings lt user account gt RECOG i
8. 294 Removing OV CN ceca as aa a a acts stan EE A aaia 120 Registration and Management of Gene Cluster Sets o cccccccccecesessssccessesssessssesesesesseeevavavessesevavavenseseees 121 30 1 Registration of a POTS cluster SSL papalecaineserasantivciaraienwncnes entra eabierieiaearsiuisenavsininidiesienadonmmemnenniebande 121 30 2 Outputting a gene cluster Set tO a FIC ee cccesesesesssessesesescscecevsceeescevevsvevesevaveveneetseevavaveveneeeeeetans 124 30 3 Editing a gene cluster set removing ZENES cccsecsscesecsesescsesecessesecersesececsessvsesecaeeesavecsesesaceeseceeseees 124 30 4 Registering additional genes clusters to a gene cluster Sti eecececececeseseecesesesseseeseteeeseeeaees 125 30 3 Removing a gene SIE oe aca sraraictsatcroannateressencnnrenasaniatnad nericanionnmmnatenaidatqaiaaenanieinemolatinnen 125 30 6 Referencing the list of gene ClUSter SOS eeecesssscsesessecscecesesesesvaveveveceeeetevaveneseetevavaveveneeeetanans 125 PNM E acacia cts vac AEE E vo epee piesa A ev eves cea acess esa sae esses R E AA A vars A 127 31 1 Registering a combined Se t osoeeoseseeeeeeeesneneserererunerurerurnrururururururisrsisknrsnsnsnnnnknrnnnnnnnrannrununnrunun nenene stusads 127 3 t2 Editing a Combed SEE raii aE 130 silo Remove a Combined n Cope one SP Pcs ee re ee 130 31 4 Specifying a combined set as a filter condition woe ccc cccee ces ceseeeeeceeceseesesseeeesessensaveeeessenenees 130 31 5 Specifying a combined set
9. E Gackyround color tor outgroup cess P C Background color for outgroup cells considered to be ingroup Background color for selected ine cetis 1 E Background color tor setected ine cets 2 JE Background color for search resut cells RECOG Client User s Manual 2 On the PPM tab the background color of the cells the display nondisplay and the color of the boundary are set Color for border line The color of the boundary between cells is set Untick and the boundary is not drawn Background color for ingroup cells The background color of the ingroup cells is set Background color for outgroup cells The background color of the outgroup cells is set Background color for outgroup cells If the horizontal transfer option is specified the considered to be ingroup background color of the outgroup cells that are considered to derive from the ingroup is specified Background color for selected line cell 1 The background color of the cells of the selected cluster is specified Background color for selected line cell 2 The background color of the cells of the selected species is specified Background color for search result cells The background color of the cells of the searched cluster is specified 3 Click the Apply button 4 To enable disable the color settings of the PPM cells double click Color Base Color on the control panel 11 6 Color change according to the gene count within a cell The bac
10. IK Bacillus cereus ES In Basmus cereus NYH 391 98 IE Beciius ihuringensis serovar koniiuiiaon 97 27 In Basmus thuringiensis Al Hakam IR Bactius clousd KSM K16 vee Mesie Uatethmene Om ear Bacillus amyhiquetaciens FZB42 Socilus cereus ATCC 10997 95 RECOG Client User s Manual 25 3 Editing species group names 1 Select Sp Group on the Selected tab 2 Select the species group to be renamed in the lower view click the right mouse button and click Rename Rename screen is displayed 3 To rename the species group edit the name on the Rename screen and click the Apply button 25 4 Removing species groups and removing species from a species group 1 Select Sp Group on the Selected tab 2 Select the species groups or species to be removed in the lower view click the right mouse button and click Delete 96 RECOG Client User s Manual 26 Genome Core Structure Alignment CoreAligner Genome core structure analysis consists of the extraction of genomic structures that are well conserved among related genomes That is a pair of orthologous groups are extracted whose genomic neighborhood relationship is conserved above a certain level and the orthologous groups are realigned based on this neighborhood relationsships The CoreAligner program for such analysis is run on the RECOG server and the extracted core structures are displayed 26 1 Running the CoreAligner program
11. Switching the RECOG OEE rr oss scenes ererncieesteteaorstee sled niccede nnocen 29 7 3 Reference to the registered RECOG servers ooocicieccececccccescescesceseesescessesssseeseseeseuseseessesensessevensenseeees 29 TA Registering the REGOG SQV 60 wicsiiciscesiicesiciacciscsceieisuiienstaccsadsacsiystanssiacustdecaneabdguddnedsbensiacdstantaatibdjecinadstacsindes 30 7 5 Editing the RECOG Servebuuui iccccecccccccscescecescsscessecessesseeeeseuseesueeeseasavseseasevseseuseuseveeseeseusesseseusesevessensenees 30 10 Rom val or the RECOU Gyor enine AE aaa 31 Display and Manipulation of the Taxonomy BrowSer aeeseseseeseeseeeeeseruorreereusrrisiensnrisnersnsrsnsrererererererernns 32 8 1 Expansion Collapse of the Taxonomy Tree wue e ciccceccsesssssssesssessscssesesesescsvsvevssesesssvavesesteeevavavensetseetaneven 32 8 2 Specification of a set of classification ranks to be displayed on the Taxonomy Tree 32 8 3 Specification of the INGrOUD OUTZLOUD cececesescssscececesesescececeveceecsesvavaveveceecetevavsueseesevavaveveeeetevavaveveneeeatens 33 8 4 Automatic IZFOUD OUTPFOUD specification smsisisctssuniniicsssshcisiitsvavcanntsnnchasecsiscaniiavndsainenadavntcasiativadiaraekeauanes 34 Ortholog Clustering DOMCIUSE uu cseessscsssssscesscsscessccssessssesessescssesesesssseseseasseeseccsnesssesteassnsteassesteaesteseststeataee 36 SR Ce Nae 4 12 colo ae ree EE ee nee A eran eee aS ee eT 36 Ta ECCU OF Bog OLD Col emer terre eee errr a tremor ee t
12. and specify the ClustalW conditions on the Multiple Alignment tab on the Option screen Taxonomy Tree PPM Function Category Color Neighboring Clusters Mutiple Alignenert Tree General Path C projectm eclipse recog_clent clustatw exe Options TYPE Use defout v OUTPUT OUTORDER MATRIX SEGNO RANGE lchastal v fasaned v olosum v FF v START GAPOPEN GAPEXT GAPDIST 100 02 GUICKTREE ON OFF KTUPLE VANDOW SCORE 1j 5 percert v PYVONAMATRIX PYVGAPOPEN PYYGAPEXT lolosurn v 100 04 Path Specify the path of ClustalW The default setting is the ClustalW attached to the installer 83 RECOG Client User s Manual TYPE Use the default Multiple alignment is executed with the default parameter of ClustalW Protein Multiple alignment is executed as per the setting specified on the screen 2 Inthe Disaggregate Mode select the cluster in the cluster information display table on the Info tab click the right mouse button and click Multiple Alignment on the pop up menu to display the progress screen and execute the multiple alignment When the Confirm screen is displayed click the OK button Info Histogram ossible aspartate transaminase aminotran Gene Name Description Cluster ID Regional Genome Map Comparison Multiple Alignment 3 After the completion of the multiple alignment process the Multiple Alignment screen is
13. 3 Saving the list of genes 1 To output the list of gene property values in tab delimiting format click the Export button on the Gene List screen to display the Save gene list screen enter the output file name and click the OK button 76 RECOG Client User s Manual 20 Display and Operation of the Circular Genome Map CGM The Circular Genome Map CGM draws a circular linear genome map of the selected species t Genome Map 20 1 Displaying the CGM 1 To display the CGM select the species on the Taxonomy Tree on the Selected tab click the right mouse button and click Genome Map Chromosome name IR Bocifus cereus E33L IE Bacilus cereus HYH 391 93 Ik alaes A in E Taxonomy gt IRE Sp Group gt EC chromosome 1 IKE Gene List plasmid p819727 e Gene order on bik Color b Ik 71 RECOG Client User s Manual 20 2 Changing the selected region 1 Enter the region to be selected in From and To in the upper part of the CGM screen and click the Show button The entetred region is highlighted and the displayed region of the genome map in the lower part of the CGM screen changes The selected region can also be changed by dragging the mouse on the circular genome 2 To move the selected region in the clockwise counterclockwise direction click the cl Previous Next button in the lower part of the CGM screen respectively It is also possible to change the moving dist
14. Clustering PhyloPatClust Execute Local Server Target Sub Cluster Cluster Use displayed clusters only gt gt Parameters Execute If the clustering is carried out locally specify Local If the clustering is carried out on the RECOG server specify Server Note Server is available only in an environment with an Internet connection Target If the clustering is carried out based on the phylogenetic pattern of a cluster specify Cluster If the clustering is carried out based on the phylogenetic pattern of a sub cluster specify Sub Cluster Use displayed clusters only If this is checked phylogenetic pattern clustering is carried out only for the clusters currently displayed on the PPM This reduces the processing time when there are many clusters 3 Click the Parameters button to set the parameters on the parameter setting screen 60 RECOG Client User s Manual 4 Click the Apply button on the Confirm screen to execute PhloPatClust Upon completion of the process a dendrogram clustering tree 1s displayed on the Clustering tab based on the clustering result and the PPM is sorted based on its arrangement 2 Phylogenetic Pattern Clustering PhyloPatClust Execute Local Server Target Sub Cluster Cluster C Use displayed clusters only lt lt Parameters PhyloPatClust Parmeters Minimum number of organisms 3 4 Miss Dist Ratio EJ
15. Each line is color coded in accordance with the conditions Color Details Black There is no insertion between genes Green There is an insertion between genes Red The relative direction of the genes is reversed inversion Gene Direction The triangular arrow in the upper part of ortholog group indicates the direction The background is displayed in the color corresponding to the typical function category of the ortholog group 99 RECOG Client User s Manual 26 4 ZO 26 6 vs ona Changing the display position To scroll the screen in the direction of the clicked button click Move Lett gt Move Right in the Toolbox on the Core Genome Alignment screen The display position can be changed by dragging the mouse on the Overview window Selecting an ortholog group To highlight an ortholog group click the ortholog group in the magnified view on the Core Genome Alignment screen Also in the Genome Comparison Viewer the corresponding ortholog group is highlighted Locating an ortholog group at center Double click the relevant ortholog group on the Core Genome Alignment screen to display it at center Also on the Genome Comparison Viewer screen the corresponding ortholog group is mainly displayed Setting a reference genome To display the Core Genome Alignment display modification screen click View View Change on the Core Genome Alignment screen In the Target column check th
16. If this column is checked the Core genes are displayed Non Core genes Genes that were not extracted by the CoreAligner analysis are called Non Core genes If this column is checked the Non Core genes are displayed RNA If this column is checked the RNA genes are displayed 109 RECOG Client User s Manual Switching options for ortholog line display Options Details Universal Only Ortholog groups that contain the genes of all species are called universal ortholog groups If this column is selected only the universal ortholog groups are displayed 1 vs 1 Only Ortholog groups that contain only a gene for each species are called 1 vs 1 groups If this column is checked only the 1 vs 1 ortholog groups are displayed Unique Only If this column is checked only unique genes that form no Non Core genes only ortholog groups are displayed 3 Click the Apply button 27 11 Changing the display style of species names 1 Click View View Change on the Genome Comparison Viewer screen Click the View tab on the screen for changing the display style of the Genome Comparison Viewer screen 2 Select the display stype of species names in the Organism column on the View tab Normal The official species names are displayed Abbreviation The abbreviated species names are displayed Show Strain If this is checked the strains are displayed 110 RECOG Client User s Manual 27 12 Display Nondisplay o
17. Nondisplay of the Locus Tae aiinnwsiunwncicnisendinvstieierrindivennedinieiveincintiveneniinnn 111 RECOG Client User s Manual 28 29 30 31 32 PLN Ba ME GT e E a gee eee eee ele Pe Pe Om Em Pee ROE Rie Oe me A PA A em Pee EAE teen Pe 111 21 14 Automatic correction of the gene Orientation cece cece ces cesceeessessesessesseeeesesseeseveesesseneeeens 112 21 15 Changing the display style of the scale MarkS woe cece ces cee ceeeeeeeceeceseesesseveesesseeseseeenseneneens 113 AR Pl se all 1 gn net en eT ete ene ROE Em Une TOE Reena Se meee eR RC TR NOR Metter meee enn Meer oer ewe 114 Updating the Gene Information asic cis tara ned aches saccid assccdgawn tes sa nnaccidiabwaicndeavinisaceasienieassvedaneeeiaenbes 115 28 1 Updating the Taxonomy Tree based on the Update notice ou ceeeeecessessessessesssssessesseseseenees 115 28 2 Updating gene information through Update Data wo cece cece ceeceseeseeseseesessevenseeeenseneneens 116 Registration and Management of Gene Cluster Properties ccecccecscsesesesssssessesesesssseseseeesseeseeeenean 117 29 1 Registration of gene DEO CTS segs sec cacc po bacs tes ac ceavetaccanneheoinasnetaracdencecectanictebdsbanenezedanniacesnansceeninants 117 29 2 Referencing a list of gene cluster Proper tie oo eecceseseseccssecssesesessesssessseseesssevevesesseveveneseneeeetanes 118 p20 We EAE 01 6 6 i af 05 pee oO tor cr Ra ren reer net EERO VE REUSE CRE RE RON RU eos ee maT Ree 120
18. REAM_OOOD10 REAALOOOOED FSIALOOOOE REAM_OOO100 RBAAL_OOGDISO FETAL_OOCeS FEREM_O0OS 0 REWLOO03D REAU 0903S OOD IC_ICoIL__ Secs sist Ls G SS 0 A i o Omen FAFELOOD 10 REAM_OD0170 REALIZZO PEAM_000190 REAM 000200 FEPAL_OSS1 REAM O09210 REAM 033160 Bacillus anthracis Serne 5222084 45011 FAMR 225 1 tasiga TAAA BAS0WDI BASWDIS BASIQ BASO0OS TRAA ILE BASODIT BASODIS TRA SER 1 BASIOZI TERA ALA A BASODOS BASIOUG REHA IGS 1 REHA SS 1 BASDOIA BASDOZUBASOOZZ TFNA ILE 4 BASIOZI BASODSS GAS OCCA SE a CO i ieee Coot Cj man 0 Byen0NS BaOO17 pasos eistis besO019 Bacillus cereus ATCC 10987 5218705 45012 ECE_5 7S3 BCE OMA ELE 0023 ECE 0034 BLE O02 BCE _Seat BCE 001A BLE_OO21 BCE SELI BLE OMS CEMS BCE 00I BLE 5738 BCE 0010 BLE_0013 ECE_ODIS BIE 0023 SCEO Bie 0022 BLE_O002 BCEL00OS SCELSSA BLE_OOOSBLE_OOTI ECE SSA BIE DOOBLE MOS SCE Bte cozi ete BE00Ol ECE BLE _COO7 BCE S740 BCE O12 BLE _0019 BLE 0022 BLE _S643 BCE S743 ECE_0OS BCE _O0GEE Bee LILI eS oo CD een ee Go Oj n BtE_OOKS BCE OCS 21 1 Displaying the RGM 1 To display the Regional Genome Map RGM screen select a cluster on the Info tab click the right mouse button and click Regional Genome Map on the pop up menu Info Histogram lutamine amidotransferase pdxT SNO family Cluster ID Gene Name Description 09441 yaa Regional Genome Map Comparison Multiple Alignment RECOG Client User s Manual ACOs Zi 21 4 Zooming in o
19. Server screen enter the URL of the RECOG server and click the Apply button 4 On the Server List screen click the Apply button 7 5 Editing the RECOG server 1 Click File Change Server Server List to display the Server List screen 2 On the Server List screen select the RECOG server to be edited and click the Edit button The Edit Server screen is displayed 3 On the Edit Server screen enter the URL of the RECOG server and click the Apply button 4 On the Server List screen click the Apply button 30 RECOG Client User s Manual 7 6 Removal of the RECOG server 1 Click File Change Server Server List to display the Server List screen 2 On the Server List screen select the RECOG server to be removed and click the Delete button A warning message appears Click the OK button Q Delete server http test server ac jp 3 On the Server List screen click the Apply button 31 RECOG Client User s Manual 8 Display and Manipulation of the Taxonomy Browser The Taxonomy Browser displays the taxonomy tree of organisms On the tree manipulations can be performed including the selection of the ingroup outgroup to be subjected to DomClust analysis The Taxonomy Browser comprises the All tab for specifying the species group to be subjected to analysis from among all the available species and the Selected tab for specifying various manipulations of the species grou
20. Set Cluster Set Combined Set Name on the control panel 131 RECOG Client User s Manual 32 Species Set Multiple species can be specified as a set The species set can be utilized for the phylogenetic pattern filtering setting the species color setting and profile editing and operation 32 1 Registering a species set 1 To display the Organism Set screen select a species on the Taxonomy Tree in the upper part of the Selected tab click the right mouse button and click Organism set New organism set Organism Set Name Organism Set 1 Target New O Overwrite O Add 2 Enter the name on the Organism Set screen In the Target column specify one of the following New new registration Overwrite overwriting of an existing species set Add additional registration 3 To display the species set in Organism Set on the set control panel specify the conditions and click the Apply button Control Sp Group Set Gene Set Gene Set Conbination Cluster Set Cluster Set Conbination Organism Set C Organism Set 1 Bacillus cereus 4H187 Bacillus cereus 4H820 Bacillus cereus ATCC 10987 Organism Set 2 132 RECOG Client User s Manual 32 2 Editing a species set name To display the Organism Set screen select a species set in Organism Set on the set control panel click the right mouse button and click Edit 1 Modify the species set name and cli
21. Tree screen the following operations are possible Reading the dnd files Click Open DND file select the dnd file and click the OK button Outputting the phylogenetic tree to a PDF file Click Dr PDF specify destination and file name and click the OK button Switching between the rooted phylogenetic tree and the unrooted phylogenetic tree To display the rooted phylogenetic tree click Rooted Horizontal and to display the unrooted phylogenetic tree click gt Unrooted Displaying the distance Click ah Show Length ON OFF 86 RECOG Client User s Manual Various settings j Option Settings lt Directory tab Set the default directory for loading DND files and the defaut directory for outputting PDF files lt Style Specify the node style lt Color Specify the Locus Tag colors Species Each species is displayed by the species color the color of the species header in the PPM table specified in the Color Organisms menu on the Texonomy Tree in the upper part of the Selected tab OUT IN Group Each species is displayed by the ingroup outgroup color specified in Font Color on the Taxonomy Tree tab on the Option screen according to the current ingroup outgroup specification 87 RECOG Client User s Manual 23 Function Category Frequency Graph Numerical Data Graph On the Histogram tab the frequency of the function category in the same phylogen
22. User s Manual 5 9 Histogram tab On the Histogram tab cluster properties are displayed in graphs of various types In normal disaggregate mode annotation information is displayed Gan mode Aggregate mode Disaggregate Bar graph for phylogenetic pattern frequency Description Function Category The description is displayed For the background color the color of the sub cluster s typical function category is displayed Value 1 The species numerical data are displayed in a bar graph line graph Difference 2 The differences in the species numerical data are displayed in a bar graph line graph nig Hayen ED i 731 633 PL 335 m ni I 97 _AD04E s37 A420 ee 3 Pyridoxine blossr bosis eroteln BIE cerS Seryi thath eyrhhetane ese thi Clycerate kirase Cid 64_AN250 64_AN042 164 A410 20 _ 4205 BCE 425s Graph display of the property value 23 RECOG Client User s Manual 5 10 Status bar The Status bar displays the amount of used memory PPM information and application update information 136M6 1065ME6 Number of Selected Genomes 15 Number of Phylogenetic Patlerns 16910 1 Display of the amount of used memory left side The amount of memory used by the current application is displayed Left side the amount of memory used by the application Right side the amount of memory allocated to the appli
23. as a Color CONITION Li eee cscs ces ceeeeeessesceeessesseveesessevenseesenseneneens 130 31 6 Enabling Disabling a filter SO CEI csan ai 131 31 7 Enabling Disabling a color SEW ccczixtcestasncichsvinnibosesaddacinianncnedbsrcacheasasadnstaschuauvsabancsaidsiuinioseeasieaniaceicusnds 131 e E aE E E EE AE 132 32 1 Registering a species Sts ursrisnidssioniied dianid niania niaaa endi diania 132 32 2 Editing a species set NAME ouw ieeccececceccescsses ces ceseseeseesesseseesessessesessesseesesesseusesesseusesesseuseseesenseusevensesseneneens 133 323 Removing a Species St anusia nee en ne STS CT Pe mura TDS ee ee Tee 133 32 4 Setting colors using a species SO escees cca acta recctem eg chateau aed nneteanonatabiticeutaaleuenttieeeeintilecs 133 32 9 Taxonomy filtering Using a Species SO ris cacaccscssccssoccasatisnteencsnanctnsscseseraerstanrsacesacncaasetasastanusigeeaneipeniae 133 RECOG Client User s Manual 33 Similar Phylogenetic Pattern Search aana A aA E Eai 134 33 1 Profile registration TVONICS i gs eco sc ccs scnencustasucccupascdacnsenaccxancdsedecaesseccksniceactnauedansetsaaceeiacs 134 Se Me AIM et OE ccat sect caer eiscee sce Acacias deie cg cate EA EEAO NAATA 135 a REMOVE a WOE accent TE 135 33 4 Similar phylogenetic pattern searCh eeseseeeseeseseeseeerserisrersnersnsrsusrsnsrsnsrsnnrnrunurunnrneurunnrneuruenrnenrnennnn 136 33 5 Uses of the results of the phylogenetic pattern similarity Search eeeeeesesseeeseeeeeeeee
24. click File Update Data 2 Select one of the following on the Update data screen and click the Apply button Update data Update data Updated data only Updated data only Force All data Taxonomy data only Only the Taxonomy Tree data are updated Other data are retrieved as the need arises Usually this mode is the most efficient Updated data only Regarding the Taxonomy Tree data and the gene information currently held by the RECOG Client only the data updated by the server are updated This function is used to update necessary information collectively Updated data only Force The Taxonomy Tree data and all the gene information held by the RECOG Client are updated This function is used to force an update in cases where the RECOG Client s information is defective Alldata All the gene data are downloaded Note If All data is specified it may take about several tens of minutes to download the data depending also on the network transfer rate 116 RECOG Client User s Manual 29 Registration and Management of Gene Cluster Properties It is possible to incorporate any type of gene information by importing gene property files Cluster properties are properties defined for each ortholog cluster which typically calculated using gene properties Gene properties and cluster properties can be utilized for various analyses such as sorting and PPM coloring 29 1 Registr
25. is displayed in the color specified by the user in Color on the control panel Genome Map Options Function Category Function Cetegory on Category ee tr 1 Amino acid biosynthesis 1 7 Histicine family 2 Purines pyridines nucleosides and nucleotides ener Positive Negative Positive Negative ME Use the coke of the control tres 20 5 Displaying gene information in a browser i Double click a gene on the genome map in the lower part of the CGM screen to display the information on the default external resource specified in 35 External Resource URL Management in the browser Click the external resource URL displayed upon right clicking and the information on the external resource is displayed in the browser 19 RECOG Client User s Manual 21 Display and Operation of the Regional Genome Map RGM To allow users to compare the chromosome map around the genes belonging to a specified ortholog cluster the Regional Genome Map RGM displays the genome map where these genes are arranged at the center thd Alinment List Pa j a Bacillus anyloliquefaciens FZB42 33913340 45341 REAY_ OWDSD REAL CONTO FRPAOWSO FOAL FEAH OCOOAO REALU 030140 REALL OI02GO FRPH_OOOS4 REALLUDIQADE REALL OCO0SO RBAL 090159 REA OOOI ROAU COUSO RALL 090359 REWAL OO0SS0 REALL OCOOCO RSALLCOOITO REAL COUJSIRSRA 00120 REALL OIO1ICO FBA 00a FEPALOOOSIOREAM_OOOSSO 86 REAULOO0
26. meee te ene ee eee OUT Peer To ene Ent EO PeE on nena oe ere eee eee ere ees 91 24 Clustering Neighborhood a lt 1 gt aoa ene ee ee eon se Pe PR Pe 92 24 1 Execution of the clustering of neighborhood genes uo cesceceesessesceseesessesesessessesssessessessnses 92 Display Nondisplay of the clustering results ca ccscccccscccsccccscssssecescsesaseceeasseacenscssensesvacevssatceaesvenesssentsitsstoasseieas 93 24 2 Changing the color of a group of neighborhood GENES eee ees ces cseeseecesseseesesseseesssesseeesenses 94 RECOG Client User s Manual 25 26 ei Pe Ook ol aC gc a en ae Cena ee A EAT PT PE AT E A EEE ee Oe EP AE CT eae ne eee A 95 23 l Displaying Se secs casa a aa AES AA TATANA aT E 95 29 2 Registration of species Bi Sasi tos cis accsicssttnccat san eaaa aaia A a a Aa AN AEE ARAARA NAARS 95 25 3 Editing species group NamMesS anes eet eee een eee er aR On SS ee RO EEE OOS ene Sn RAN mre evn CN nme eae 96 25 4 Removing species groups and removing species from a species group ou eeeeeeseeseeseeeeeeeeees 96 Genome Core Structure Alignment CoreAliginer c scccscsssscsssesessesecessssesessesesseseseceesesacsesecessesevereesesieeeraesee 97 26 1 Running the CoreAligner program ciel scczccscisaitiiacesscisobdpectensiesssaidsicensecssecsutesnidesaneiddadiniebdocctebisitectieddaacucd s 97 26 2 Displaying the CoreAligner analysis results wo cece ccc ces cesceseesescesceseesesseesesesseusesseveeseuseveesensen
27. on the set control panel click the right mouse button and click Delete set combination When the warning message is displayed click the OK button 31 4 SEs Specifying a combined set as a filter condition To set a combined set as a filter condition in Filter Gene Set Filter Cluster Set Filter on the control panel select the combined set in Gene Set Combination Cluster Set Combination on the set control panel click the right mouse button and click Register filter Specifying a combined set as a color condition To set a combined set as a color condition in Filter Gene Set Cluster Set on the control panel select the combined set in Gene Set Combination Cluster Set Combination on the set control panel click the right mouse button and click Register color 130 RECOG Client User s Manual 31 6 Enabling Disabling a filter setting 1 Select Filter Gene Set Filter Cluster Set Filter on the control panel click the right mouse button and click Enable Disable 2 To enable disable each individual condition of a combined set double click the condition in Filter Gene Set Filter Cluster Set Filter Combined Set Name on the control panel 31 7 Enabling Disabling a color setting 1 Select Color Gene Set Cluster Set on the control panel click the right mouse button and click Enable Disable 2 To enable disable each individual condition of a combined set double click the condition in Color Gene
28. presence or absence of genes phylogenetic pattern is displayed as a heat map Basically species are shown in the order of appearance on the taxonomy tree but if outgroup species are specified ingroup species are displayed on the left side and outgroup species are displayed on the right side However the order of display can be changed via the operation panel In each cell the locus_tag of the gene which belongs to the cell or the number of genes is displayed When a cell is clicked the relevant cluster and gene data are displayed on the Info tab at the right end If DomClust analysis is carried out upon specifying outgroup species the cluster table is displayed as a nested table That is genes in the outgroup species form an outgroup cluster which corresponds to multiple swb clusters that consists of genes in the ingroup species All of these are included in the upper hierarchical cluster see the figure below Furthermore as its upper hierarchical cluster a homologous cluster is defined as an accumulation of homologous ortholog groups In normal disaggregate mode the function categories and gene names or cluster ID s of the sub clusters are displayed in the columns on the left side the function categories and gene names of the clusters are displayed in the columns on the right side and homologous clusters are displayed on the right side thereof These columns are called cluster headers On the other hand in the aggregate mode clus
29. results are saved to a file they can be used even if the DomClust result file is reloaded Profile column Specify the profile type lt Phylogenetic pattern Use as a profile the binary vector representing the occurrence pattern of species expressing the presence or absence of species as 0 or 1 respectively 136 RECOG Client User s Manual lt Gene property Use as a profile the numerical vector representing a property value of each gene based on the specified gene property Type of distance Specify the index for calculation to be used as the value of dissimilarity in which 0 is the nearest and 1 is the farthest lt Normalized hamming distance lt Correlation coefficient lt Correlation coefficient absolute lt Mutual information If Gene property is specified in the Profile column only the Correlation coefficient can be specified Sort by the calculated result If this is checked the PPM table is sorted using the calculated distance values 3 To set the following conditions click the gt gt Option button Treatment of missing values In cases where there is no gene corresponding to a species in a cluster specify the calculation method to cope with any missing values This setting becomes effective when Gene property is specified in Profile lt Ignore Calculate in disregard of the species lt Average Calculate by applying the mean of the values of the other genes
30. seeseeeeeeeeenenenereseresurerurururururururururuninininnntnnukannknknknknnn nunana nanunananunan aankan nnnn nanne nnana 41 11 5 Changing the PPM cell boundary Color s sessenonsenennsenenenenensenenesnenrennsneenenrernnrsnenrnnrnrennsnrnronrnrenrerreronne 41 11 6 Color change according to the gene count within a Cell ccc cee ce see sesceseeseeseseeeeeeenes 48 11 7 Color display corresponding to each functional Cate QOry eceececcee cece cee cesceseesesceseesesseseeesees 49 11 8 Aggregated display of the PPM ccc cc scecesceseseeceusesesseeseuseseeseusesseseeseueveesouseaseveeeenseneess 50 RECOG Client User s Manual 11 9 Limited display of a selected region on the PPM Wu cece cece cesceeeeeeeseeseeeeseeseveeveeeensenens 51 11 10 Highlighting a species by selecting it on the Taxonomy Tree aneen 52 11 11 Selection of a species phylogenetic pattern in a cluster e ecececesssessesesesestesesesessesesseseseceneeees 52 12 Color Display by Propertie oo icc ccccccceccsceseececeeeeseuseeeeseesevsessesssseuseveeseuseseeseuseveessesesseaseveuseusesesseuseveesenses 03 12 1 Color display setting by DLO CICS asus cas riccedancccantseacsweniccdesreiaciseteeccieievdiaedauetneawdns 53 12 2 Enable Disable property color setting avisciessarcicanitvasvonsstsarveiaiavacinatsursroenuveivet en itavduitvndtounmvdeiounmanieriia 55 To Fe O a AE T A A A AOA rare 56 13 1 PPM sort m disaggregate Mode ee ne aaa ne nr 56 13 2 PPM sort in the aggre
31. set screen and click the Apply button If Overwrite the gene cluster set of the same name is checked the registration is made upon overwriting the gene cluster set of the same name if such a set exists Registered gene cluster sets are displayed in Gene Set Cluster Set on the set control 122 RECOG Client User s Manual panel 30 1 3 1 Display the Keyword Search Result screen ti Keyword Search Result _Neene a 02956 1 5 5 adaA SCE_s772 ada A O SCE4 254_Ass4adas 6C3740 SCAHIS7 _A37iedsA SCAKS20_S7SiadaA 0292910315 09178104 0373510415 Z02415 02039115 Z 02049 1415 5 02056 1415 Z 020871015 5 02201108 29023121045 3 02707108 028221008 Z Display only matched genes M Highight matched genes a K m a m m K m 2 m m m a a 2 m a a roy story ry protein Te Registration from the keyword search results aai _ ile oreintory erotein rehire rere datory erctein tional regulatory protein 2 To display the Register _gene cluster set screen check the column to the right of the gene cluster to be registered and click the Register gene set Register cluster set button 3 To register the gene cluster set specify the set name and the destination for registration on the Register gene cluster set screen and click the Apply button If Overwrite the gene cluster set of the same name is ch
32. the Any conditions in Filter Taxonomy Filter Any on the control panel Also the species names meeting the Any conditions are displayed on the tree in light blue A name can be attached to each of the Any conditions in order to distinguish between the conditions All Selected Clustering 9 root 6 S Bacteria 6 Bacillales 6 S Bacillaceae 6 IN Bacillus cereus AH187 IN Bacillus cereus AH820 IN Bacillus cereus ATC IN Bacillus cereus ATCC 14579 IN Bacillus cereus B4264 OUT Oceanobacillus iheyensis HTES31 i 7 Li o Control Sp Group Set 9 Fitter Ga S Aur Bacillus cereus 4H187 Bacillus cereus AH820 B y Any Bacillaceae 20 0 2 Bacillus cereus ATCC 10987 Bacillus cereus B4264 To specify the Any conditions more easily select more than one species name click the right mouse button and click Taxonomy Any New For all any conditions Any 64 RECOG Client User s Manual condition shown below to display in the lower view the species names registered for the Any conditions To add species to the Any conditions select the species name or names click the right mouse button and click Taxonomy Add Any Add Additional Any condition The relevant species are added to the Any conditions in the lower view and the relevant species names are displayed on the tree in light blue All S
33. the Keyword Search Result screen is displayed The conditions corresponding to the search results are displayed in Filter Color on the 70 RECOG Client User s Manual control panel On the PPM only the searched clusters are highlighted Ed Keyword Search Result Control Sp Group ada Fitter ee E pra pa Taxonomy Filter gt Gene Organism Count Filter 4 Keyword Search Keyword Search Cluster dna Gene Set Filter Cluster Set Fitter Organism Column Sort Color Keyword search Cluster dna L703 L Jars O y rth y aR y D D i 5 5 Check Display only matched clusters on the Keyword Search Result screen to display on the PPM only the searched clusters Upon unchecking all the clusters are displayed Check Highlight matched clusters to highlight the searched clusters Upon unchecking and the highlight is cancelled Also by clicking the color setting column the color of the highlight can be set 71 RECOG Client User s Manual 17 2 Search of genes p 1 Click p Keyword Search in the Toolbox to display the Keyword Search screen On the Keyword Search screen click the Gene tab 2 Specify an item and a keyword and click the Search button To specify multiple conditions click the Add Condition button to add conditions To clear a condition click the Clear Condition button Upon specifying the condition s click the Search button bea Ke
34. the Option button on the Core Genome Alignment Preview screen to display the Core Genome Alignment Print Option screen and specify the option Core Genome Alienment Print Option Row count par one page 10 Show legend Show organisa name every row C Show page number Page setting Option Details Row count per page Specify the number of rows displayed on a page One page Print so that the Core Genome Alignment image fits into a page Show legend If this is checked the legend is displayed Show organism name on If this is checked the species names are displayed in all the rows every row If unchecked the species names are displayed only in the first row of each page Show page number If this is checked the page number is displayed Page setting Specify the paper size and orientation 3 Click the Print button on the Core Genome Alignment Preview screen and the printer selection screen is displayed Specify the printing conditions and click the OK button 26 16 Saving the CoreAligner results The CoreAligner analysis results are saved automatically in the Project directory or its sub directory when an analysis is conducted Save the analysis results in the CoreAligner format coaln 1 Click te Save Core Genome File in the Toolbox specify the destination for saving and the file name and click the OK button 104 RECOG Client User s Manual 27 Genome Comparison Viewer The Genome Compariso
35. the completion of the DomClust analysis the DomClust analysis result is displayed on the PPM When the completion message is displayed click the OK button If the analysis is executed in the background the Load DomClust file message is displayed Click the OK button Confirm Q Load DomClust file 38 RECOG Client User s Manual 9 3 Display of the DomClust analysis results The previous DomClust analysis results are displayed Size La Update Cluster 10 1237315012_08302 1 679 KB 2009 02 24 225923 Cluster Count 9334 cluster 20020213 deist 3 284 KB 2009 02 20 11 0 amp 57 Server cluster _20090224_gene_colordcist 4 294 KB 2009 02 24 9 16 53 http mbsd genowe ad jp cluster 20080327 deist 2 156 KB 200900327 14 57 32 OPtions eval 0 0010 luster sample deist 3 034 KBI2008 06 25 21346 store i 60 0 coverage 0 6 cutoff 80 0 Sim_measure score besthit none clusiwede orthology phylocut 0 5 taxonlevel none adiovlo f 8 A 2 On the Open files screen select the file filter DomClust File dclst cluster and then select a project and a DomClust analysis result file Upon selecting the DomClust analysis result file the relevant information species set and parameters on the analysis result is displayed on the right side of the screen 3 Click the Apply button on the Open files screen to display the selected DomClust analysis
36. to register it on the New Server screen New Server Server http recog server ac jp 5 When the Apply button on the New Project screen is clicked the project is registered and opened Note To register a project ensure that you can connect to the RECOG server 25 RECOG Client User s Manual 6 2 Open a project 1 Click File Open Project and click the relevant project The clicked project opens View Search Run Option New Change Server gt Gd Open file Open Project 4 Test Project Project List fas a 6 3 Reference to a list of registered projects 1 Click File Open Project Project List to display the Project List screen The registered project names and the RECOG server URL are displayed on the Project List screen Also the Select field of the project in use is displayed and checked bd Project List http Wrecog server ac jp 26 RECOG Client User s Manual 6 4 Project registration l Click File Open Project Project List to display the Project List screen On the Project List screen click the Add button to display the New Project screen On the New Project screen enter the project name and set the URL of the RECOG server that will conduct the analysis To register the URL for a new server click the New Server button and register it on the New Server screen On the New Project screen click the Apply butto
37. 20 Probability Cutoff 4 0 v Type of Distance Normalized hamming distance 14 2 Operation of the clustering tree On the clustering tree the display of distance can be switched on off and by clicking a branch point clusters belonging to points not higher than the branch point can be selected To switch on the display of distance do the following 1 Click the right mouse button on the Clustering tab and click and check Show Distance to display the distance on the clustering tree To select a cluster not higher than a given branch point 1 On the Clustering tab click a point near the desired branch point of the clustering tree to select the clusters not higher than the clicked branch point AE Selected Clustering bay bat be be ber bey b k Bt bel bho bli BIS b RECOG Client User s Manual 15 Taxonomy Filtering 15 Specify the filtering conditions on the Taxonomy Tree on the Selected tab to display on the PPM only the clusters with phylogenetic patterns that meet the conditions In setting the filtering conditions specify a set of species and conditions therefor at the same time One of three sets of species listed in the table below can be specified Of the three sets All and None are special sets with fixed conditions whereas for Any the conditions can be set freely If simply specifying a condition of existence nonexistence in a genome use All No
38. 21 2 Deoxyrbonucieotida metabolism 2 2 Nucleotide and nucleoside intercorrrersions 2 3 Purine ribormciectide biosyrithesis 2 4 Pyrimidine ribonucleotide biosyrthesis 3 To change the functional category color on the lower list click the Color column specify the color on the displayed Color palette screen and click the OK button 49 RECOG Client User s Manual 4 Click the Apply button 11 8 Aggregated display of the PPM In aggregate PPM mode clusters of the same phylogenetic pattern are aggregated into a single line 1 Click ap Aggregate Mode in the Toolbox to display the PPM in aggregate mode 2 The PPM can also be displayed in aggregate mode by clicking View Aggregate Mode or by clicking Aggregate Mode after right clicking the PPM tev bru gta To exit from the aggregate mode do the following 1 liek D Disaggregate Mode in the Toolbox to exit from the aggregate mode 3 One can also exit from the aggregate mode by clicking View Disaggregate Mode or by clicking Disaggregate Mode after right clicking the PPM BERR E BE PRET EE RECOG Client User s Manual 11 9 Limited display of a selected region on the PPM The limited display of a selected region is possible by dragging the mouse on the PPM to specify the region To exit from the limited display mode click the right mouse button and click Limitation Release on the menu accB Select Oreanism gee
39. 29 4 Removing a property To display the Gene Property Cluster Property screen click Option Gene Property Cluster Property List On the Gene Property Cluster Property screen select the property to be removed and click the Delete button When the Confirm screen is displayed click the OK button To remove the property click the Apply button on the Gene Property Cluster Property screen 120 RECOG Client User s Manual 30 Registration and Management of Gene Cluster Sets Multiple genes clusters can be registered as a set The registered gene cluster sets can be utilized for sorting color setting and filter setting 30 1 Registration of a gene cluster set A gene cluster set can be registered by the following three methods Registration from a file Registration from a cluster selected on the PPM Registration from the keyword search results 30 1 1 Registration from a file 1 Create a gene cluster set file The format for the gene cluster set file should be one of the following three a dclust format The dclust format should comprise the following lt Species code gt lt LocusTag gt t lt Species code gt lt LocusTag gt lt Species code gt lt LocusTag gt Example ban BA0001 ban BA0002 bca BCE_0009 bce BC0013 0inOB0010 b clusttab format The file format should be one of the following lt The clusttab format output by clicking File Export lt The fi
40. 8 082131 ack ERRELE CE 3635 BCSB IS GK 194 GTNG_1I206 IB16S ia BAS2536 BCE 2504 BC2779 GRO 10 GTNG_061 acoA The display nondisplay of the color presentation can be switched on off by ticking unticking Show color genes by properties on the pop up menu on the PPM occ anoa pean Sort b Select Organism wv FH Neighboring Clusters w Bm Color genes by properties ee Histogram Ageregate Mode Show color genes by properties 12 2 Enable Disable property color setting 1 To enable or disable the property color setting double click Color Gene property on the control panel 99 RECOG Client User s Manual 13 PPM Sort The PPM can be sorted and displayed according to various conditions based on the phylogenetic pattern 13 1 PPM sort in disaggregate mode In the disaggregate mode the rows are sorted for each cluster or sub cluster ban bat bea tee sho gta oih dm A uAN BAsoo01 BCE 000 ediad GTNG_O00 C000 daak dral E Ceo ere nare Select Organism Gene order or ban 358 Neighboring Clusters Phylogenetic pattern lexical order ee Phylogenetic pattern similarity based on the chaster 1071 BES Cole cones by properties Phylogenetic pattern clustering PhyioPatChist rd Gene properties Helam gt r fgereesic Mode 1 Ifthe DomClust result contains an outgroup click the Cluster Mode Sub Cluster Mode button in the Toolbox to s
41. Add gt __ Genome Map gt Control Gene List Cancel 15 7 Enable Disable conditions an Selected Clustering root 6 I Bacteria 6 H Bacillales 6 9 Bacillaceae 6 IN Bacillus cereus 4H187 IN Bacillus cereus AH820 IN Bacillus cereus ATCC 10987 IN Bacillus cereus ATCC 14579 IN Bacillus cereus B4264 OUT Sp Group Fitter O Taxonomy Filter a S anc Bacillus cereus 4H187 Bacillus cereus AH820 9 None 1 Oceanobacillus iheyensis HTE831 E amp Any Bacillaceae 20 0 2 Bacillus cereus ATCC 10987 Bacillus cereus B4264 1 In Filter Taxonomy Filter on the control panel select the conditions click the right mouse button and click Enable Disable to enable disable the selected conditions 15 8 Removal of conditions 1 Select the conditions in Filter Taxonomy Filter on the control panel click the right mouse button and click Delete to remove the selected conditions 68 RECOG Client User s Manual RECOG Client User s Manual 16 Filtering by Gene Count Species Count in the Phylogenetic Patterns Set a threshold value for the gene count species count in the phylogenetic patterns and filter the data based thereon The results are displayed on the PPM 16 1 Setting the conditions 1 Select Filter Gene Organism Count Filter on the control panel click the right mouse button and click Gene Organism Count Filter to display the Gene
42. COG Research Environment for Comparative Genomics is a workbench software program which is used to conduct comparative genome analyses on a massive scale The main feature of RECOG is the function of ortholog analysis between genomes of numerous species based on the display of an ortholog table rows ortholog groups columns species RECOG can also conduct various comparative analyses for detailed examination based on this table RECOG was developed based on the MBGD Microbial Genome Database for Comparative Analysis RECOG is a dedicated client software program that is available immediately after connecting to the MBGD server Meanwhile the analysis of newly determined microbial genomes eukaryotic genomes efc that are not included in the MBGD can also be conducted in a local environment by installing the RECOG server locally The latest version of RECOG is available from http mbgd genome ad jp RECOG This manual explains how to use the RECOG Client software program Organisms MBGD Web a MBG RECOG Client User s Manual 2 Operating Environment of RECOG 2 1 Operating system Mac OS 10 3 and upward Windows XP Vista Linux 2 2 Compatible Java version Java 1 4 and upward Note Make sure that Java JRE 1 4 and upward is installed before installing the RECOG Client software program If it is not installed install Java JRE 1 4 and upward before installing the RECOG Client software program
43. Gene properties file and select the destination for registering the gene property a He Dv CI Open file Horizortal Zoom Open Project ba H Save Cluster file Select OomClust file Gene propety file gt Current Project mat 15 Export Global Pace setup ee indata Nata Select the destination from among the following Current Project project name Register the gene property so that it becomes available only in the current project or in the specified projects Global Register the gene property so that it becomes available in all projects 3 The Import gene property file screen opens To register the gene property specify the gene property file created and click the Open button 29 2 Referencing a list of gene cluster properties On the Gene property Cluster property screen the registered properties can be checked 1 To display the Gene property Cluster property screen click Option Gene Property Cluster Property List 2 To display a gene property click the Gene tab and to display a cluster property click the Cluster tab The details of each screen that can be displayed are as follows Name property name 118 RECOG Client User s Manual Type type Multi multiple attribute value flag If this is checked the gene has multiple attribute values Location location for storage Gene properties only lt G
44. Neighboring Clusters a age Color genes by properties nocd CE SE Histogram Pgcrecate Mode acet A1132 B Limitation Release 5 RECOG Client User s Manual 11 10 Highlighting a species by selecting it on the Taxonomy Tree Select and click a species on the Taxonomy Tree above the Selected tab to highlight the relevant species on the PPM Also to exit from the species selection mode on the Taxonomy Tree do the following Windows Linux Ctrl left click on the selected species Mac Apple key left click on the selected species Al Selected mie O fe O Sp Group Ska IN Bacius cereus ATCC 10567 IN Bacus cereus ATOC 14579 IN Bacus cereus ESIL IN Bac us cereus NVH 351 99 S 99 foa turngensis 2 IN Bac us thuringiensis serovar ko ik Bac us thuringiensis Al Hakam 3 OY Btu chuiii IN Bocdus clausi KSM KIG B S Estus haiodurans 1 1 Botma habdrans C 125 S OY Bacius kchenitormi IW IU Gocis bcherilomis OSM 13 ATOC S OY Boctus p ft al ae wee oS L 5 11 11 Selection of a species phylogenetic pattern in a cluster The species in a cluster specified on the PPM is selected and displayed on the Taxonomy Tree on the All tab Selected tab This function is useful when searching a phylogenetic pattern similar to that of a specified ortholog group etc 1 Click to select a cluster on the PPM 2 Click the right mouse button on the PPM and click Select Organism on the pop up menu
45. Organism Count Filter screen Oreanism Gene Count Filter Sp Group Fitter Taxonomy Filter or more Gene Organism Count Fitter cs eels Gene count Cluster count Filter Gene 4 orless 0 a lt Enable a lt Disable v or more 2 2 Specify the conditions on the Gene Organism Count Filter screen and click the Apply button to display the conditions in Filter Gene Organism Count Filter on the control panel 16 2 Enable Disable conditions 1 Select Filter Gene Organism Count Filter on the control panel click the right mouse button and click Enable Disable 69 RECOG Client User s Manual 17 Keyword Search Regarding the cluster results both clusters and genes can be searched The gene search is conducted in concert with the RECOG server Search of clusters Search of genes Search Representative gene name Gene properties provided by the target Representative description of each RECOG server description gene name cluster etc Gene cluster properties registered through the use of the import function etc 17 1 Search of clusters 1 Click 7 Keyword Search in the Toolbox to display the Keyword Search screen 2 On the Keyword Search screen click the Cluster tab 3 Enter the keyword s in the Keyword s column and click the Search button to begin the search Ba Keyword Search 4 Upon the completion of the search process
46. RECOG Client User s Manual Client User s Manual Ver 1 0 7 Octover 15 2009 iF RECOG Client User s Manual Table of Contents aTa Se gcse cece ET cco cece E AE E E EE 9 1 1 What is RECOG asinine aaiae asaan iaai eiaa aaae urate aneeciec Easa aaE aaa aoaaa Eaki 9 Operating Environment of RECOG css octcsesivcsctncascaietorsedcbeanscpecavdndesisdnlacgecclosesscesicdadadscensaisiooniaseneaetedeeniecs 10 BM csc kc S a cece NAANA 10 2 2 Compatible Java VersiON eee mene een mn e OO Ue ae cere re eee ne ere meee ee neerT 10 inetalkanorny Unin alato tcc cceacn ceca a aa aaiae aai 11 J1 etalatonof REGOG for WIndows sisareen n er oe te ee eet 11 32 IMAM Nid or RECO G Tor MaG cance cece cece acco scarcesevesearequcecaaocoscceconesceesuceayaesosovessucanseteteeeesaysueeeiesnees 11 3 3 Installation of RECOG for LIMUX cccssssscseesssscssescesssssssssssenseecsnscessesesessssseeseaesessenssesseseesensseraearseseesseses 11 Of Unmstallation of REG OG fof WINdOWSssinssmsrenniamncesnasaniianns enced 12 3 5 Uninstallation of RECOG for Ma0 eee eceaciczsacessan te searecpceceaianesicastavavirastadonntoneemeviasieseattesuane anana ees 12 3 6 Uninstallation of RECOG for Linux sescess cccncececetdectecocescnpescasoeseitcetd en deodhitviedesnatetieeilinemceiecsaeeeee eatin 12 Startme and Terminating RECOG oinaan a Aa a a AER REE 13 Ae a E C SAA E A EAA E AP EAT AE AATE E N E A 13 A Terminate RECOU zeuria aE a E TAANE ANADA NARREN en NOTE nS
47. able on the same genome belong to a neighborhood gene cluster Note that the same color may be used for different clusters cells in different genomes or cells far away from each other are not related even if they have the same color in the table Display Nondisplay of the clustering results 1 To switch between display nondisplay double click Color Neighboring cluster on the control panel Sp Group Fitter Organism Column Sort Color Neighboring cluster Cluster 5 Range 5000 Gene Set Cluster Set Gene count 2 Base Color Phylogenetic Pattern 93 RECOG Client User s Manual 24 2 Changing the color of a group of neighborhood genes 1 To display the Option screen click ae Option in the Toolbox On the Option screen click Neighboring Cluster Ei Option Taxonomy Tree PPM Function Category Color Neighboring Chester suttiple Alignment Tree General Coler pattern for clustered cells 2 Set the color pattern Color pattern for clustered cells Set the color pattern for coloring genes clustered by neighborhood gene clustering The color is assignmed to the neighborhood clusters in accordance with the order specified on the list The assignment is repeated from the top of the list after reaching the end of the list Add button Add a color pattern Delete button Delete the color pattern selected from the list Up button Down button Shift the s
48. am The Histogram tab is used to create graphical representations based on the gene property numerical data Taxonomy Tree Pane Whether or not to display the taxonomy tree pane is specified Function Category Pane Whether or not to display the function category pane is specified 5 3 3 Tool menu Tool Run Option Keyword Search Organism Gene Count Filter Keyword Search A keyword search is conducted regarding the gene cluster properties Organism Gene Count Filter The filtering conditions are specified based on the gene count species in a cluster 5 3 4 Run menu Run Option 9 Ortholog Clustering DomClust es Phylogenetic pattern clustering PhyloPatGlust 9 Core Genome Alignment CoreAligner w H Neighboring Clusters Ww Ortholog Clustering DomClust DomClust analysis is conducted Phylogenetic pattern clustering PhyloPatClust Phylogenetic pattern clustering is carried out Core Genome Alignment CoreAligner CoreAligner analysis is conducted Neighboring Clusters Neighboring gene clustering is carried out 17 RECOG Client User s Manual 5 3 5 Option menu Option URL Gene Property Ve Option Gene Propety Cluster Propety List Gene Set Cluster Set List Properties The option screen is displayed The URL for displaying genetic information from an external resource is set The list of registered gene properties cluster properti
49. an external resource Name the URL and the gene property Key to be used as the key for the URL To embed a gene property value in the URL enter lt number gt in the URL click the Add button and specify the gene property in the Key column Example MBGD gene data URL http mbgd genome ad jp htbin RECOG RECOG _gene_info_frame pl spec 1 amp name 2 142 RECOG Client User s Manual 2 25 1 Gene property Organism 2 Gene property Locus Tag To display the registered external resource URL on the URL screen click the Apply button on the Edit URL screen Click the Apply button on the URL screen Editing an external resource URL Click Option URL to display the URL screen To display the Edit URL screen specify the external resource to be edited on the URL screen and click the Edit button On the Edit URL screen edit the external resource information On the Edit URL screen click the Apply button On the URL screen click the Apply button Removing an external resource URL To display the URL screen click Option URL On the URL screen specify the external resource to be removed and click the Delete button When the Confirm screen is displayed click the OK button On the URL screen click the Apply button 143 RECOG Client User s Manual 36 Appendix 36 1 DomClust parameters Parameter Cutoff BLAST E value Cutoff DP score Cutoff PAM distance Cut
50. ance on the pop up menu upon right clicking the button 3 To zoom in zoom out on the selected region click the Zoom in A Zoom out button in the lower part of the CGM screen respectively By right clicking on the button the zoom ratio can be changed on the pop up menu 20 3 Linkage between the PPM and CGM 1 Click a gene on the genome map in the lower part of the CGM screen to select on the PPM the cluster to which the clicked gene belongs 2 Click a cell on the PPM to highlight the location of the clicked gene on the circular genome on the CGM Also the displayed region of the lower genome map changes and the clicked gene is displayed 3 Click the header in the upper part of the PPM to change the genome displayed on the CGM You can compre the locations on the chromosome of the genes in a given cluster between genomes by selecting a cluster and switching the displayed genome one after another 20 4 Changing the color of genes LCI Option in the Toolbox on the CGM screen to display the Genome Map Options screen 78 RECOG Client User s Manual 2 Specify the gene color Function Category The gene is displayed in the color corresponding to the representative function category of the cluster to which the gene belongs Positive Negative The gene is displayed in the color corresponding to the direction of the gene Use the color of the control tree The gene
51. ation of gene properties 1 Create a gene property file The format of a gene property file is as shown below The first row describes the header lt In the first column sp a three letter code for a species is given and in the second column locustag is given lt In the third column the arbitrary gene property name and type are given Example If the gene property name is Expression and the type is numerical the description should be Expression Num The following four types of gene properties can be specified Type Code Example String type Char BC2639 Numerical type Num 10 3 Enumeration Enum elementl element2 Yes No type element possible value that is only Enum Yes No that is Yes the element specified here is assignable and No are the specified as a value elements Hierarchical Hierarchy EA type In the second row gene property values are described lt In the first column a three letter code for a species is given and in the second column Locus Tag is given lt In the third column arbitrary gene property values are given If a gene has two values the type should be specified as Multi and the two man values should be delimited by semicolon 117 RECOG Client User s Manual Example sp locustag GO Char Expression Num Pathway Char Multi ban BA0001 Cellular component 2000 Glycolysis Gluconeogenesis Citrate cycle 2 Click File Import
52. axonomy Tree The Taxonomy Tree shown on the Selected tab z 147 RECOG Client User s Manual Function category Functional classification attendant on and characterizing genes and clusters G Gene Property Property values associated with each gene which can be given by the user Genome Comparison Viewer A genome map in which the gene core structure is colored based on the results of DomClust analysis and CoreAligner analysis Ingroup The set of target species in phylogenetic analysis In the DomClust analysis ingroup species is specified as the set of related species on which the attention of the user is focused M MBGD http mbed genome ad jp Microbial Genome Database for Comparative Analysis which is the standard genome database in RECOG N Neighborhood gene clustering A method for identifying genes that are located near both in the phylogenetic pattern map and in the genomic sequence O Ortholog group cluster A group of homologous genes made by clustering based on the orthologous relationships between genes In RECOG ortholog groups are constructed by the DomClust program and an ortholog table created based on the ortholog groups is used as a basis for any comparative anaylsis In the genomic core structure analysis a core structure alignment is generated by reordering ortholog groups based on the conserved gene order along each chromosome Ortholog table A table showing orthologous relationships amon
53. c the information on the domain boundary and other types of information are lost To reload the analysis result into RECOG save it in DomClust format 9 5 1 Storing a file in DomClust format 1 Click H Save Cluster file in the Toolbox to display the Save Cluster file screen 2 On the Save Cluster file screen specify the file name and the destination folder and click the OK button 9 5 2 Storing a file in tab delimited format 1 Click aE Export in the Toolbox to display the Export screen 2 On the Export screen specify the file name and the destination folder and click the OK button 41 RECOG Client User s Manual 10 Control Panel and Set Management Panel On the control panel the filtering settings alignment sequence settings and display nondisplay settings for species sort settings color settings and phylogenic patterns can be specified Also on the set management panel the gene sets cluster sets combined sets and species sets can be managed Sp Group Fitter Taxonomy Filter Gene Organism Count Filter Keyword Search Gene Set Filter Cluster Set Filter Organism Column IN Bacillus cereus 4H18 IN Bacillus cereus 4H620 IN Bacillus cereus ATCC 10987 IN Bacillus cereus ATCC 14579 IN Bacillus cereus B4264 OUT Oceanobacillus iheyensis HTES31 Sort Category gene name Color Cluster Set Gene Set Keyword search Gene Descritpion aminogly G
54. cation 2 Display of PPM size information center Left side the number of species shown on the PPM Right side the number of clusters or total number of phylogenetic patterns in the aggregation mode shown on the PPM 3 Update information right side The update notice icon is displayed on the right side of the status bar when any application or public data is updated The update information is accessed by clicking this icon Infor mation i RECOG Client Version 0 9 148 Released You can get from the download site Inthe future this message should not be displayed TAR 24 RECOG Client User s Manual 6 Project Creation and Editing A Project is a saved collection of related analysis results In default mode the default project is selected and all analysis results are stored therein It is advisable to create a dedicated project before proceeding with any analysis 6 1 Creation of a new Project 3 Click File New New Project The New Project screen appears New Project Name Test Project Server URL http imbgd genome ad jp v 4 On the New Project screen enter a project name and the URL of the RECOG server that will conduct the analysis The RECOG server can be selected from the menu from among all the registered servers If an official server is used the default settings do not have to be changed To register the URL for a new server click the New Server button
55. cesaevesisicornscnmnacicanaicttovasaleiunnaicaasutieig eee E ea 81 21 3 Display Nondisplay of the Locus TaB ac aricsncatvevnoiesssececnseianacnesceavunnintniestausenveciaunavenisuetbieuaagntensionvataciains 81 21 4 Setting the gene COlOK cece cece cesceeceessseesecseseuseeseseuseeseveesessevsesesseusevesseuseuseseeseuseuseseusessevesseuseesesenses 81 21 5 Displaying gene information in a Web DrOoWSe lL cece cece csseeeseeesesceseesessessesesseusesseseeseuseseeeeusasseees 82 22 Multiple Alignment and Phylogenetic Tree wu cccccccccccccescscescscsscesseeeeseeseesesesseesessesesseuseveeseuseusesesseusevsesenses 83 22 1 Execution of multiple alignment ce i eee Sema catcecurente ce ace dewininechnciecestt tee euem de eameeatbneca cna ubeinevedeciens 83 22 2 Changing the colors of the amino acid letter Strings cesses ces ceceseesesceseesessessevesseuseeseeseses 85 22 3 Displaying the phylogenetic ab 8g lt enn ee er ae ont oP noe en Pe ee 85 23 Function Category Frequency Graph Numerical Data Graph ou eeeeseseseeeeseseseseeteteeseseseeeeeeen 88 23 1 Function category frequency graph wu eecc ccc ccsccee ces cesceeeesesseseeseesesseveeseuseuseseeseuseuseseusesseeesseuseesesenses 88 23 2 Displaying a numerical data graph a description or the function category 88 23 3 Switching between the display nondisplay Of the wo ceecsssesesesessesesesesesssseveseseseseeteteveseeeaneneeen 90 PROB Mig oe at 19 eo 9 nner ene ee
56. ck the Apply button 32 3 Removing a species set Select a species set in Organism Set on the set control panel click the right mouse button and click Delete organism set When the warning message is displayed click the OK button 32 4 Setting colors using a species set 1 In Organism Set on the set control panel select a species set click the right mouse button and click the sub menu of Color organism For the color setting method for species refer to 11 4 Species color setting 32 5 Taxonomy filtering using a species set 1 In Organism Set on the set control panel select a species set click the right mouse button click Taxonomy and click the condition menu for the phylogenetic pattern filtering For the operation procedure of phylogenetic pattern filtering refer to 15 Taxonomy Filtering 133 RECOG Client User s Manual 33 Similar Phylogenetic Pattern Search Register a reference phylogenetic profile to evaluate the similarity between the profile and the phylogenetic pattern of each cluster The results can be utilized for color setting filtering sorting etc 33 1 Profile registration from a cluster 1 Select a cluster on the PPM click the right mouse button and click Create phylogenetic pattern The Register phylogenetic Pattern screen is displayed and phylogenetic patterns according to the presence or absence of genes in the selected cluster are displayed thereon Reg
57. dacialnuierakewnen 104 26 16 Saving the CoreAligner results oo ccccc cece scescesescescesesesceseseesesseuseseesesseveesauseveesauseveesensesseneeeess 104 Genome Comparison Viewer etc ites ts cng ccs eee reenter 105 27 1 Displaying the Genome Comparison Viewer uu cccceccesccseesescesceecesescescessecescessesesseseseeseesessevensessensneens 106 21 2 Ghanginge the display dees gt Reena en eee nn ee eno ae ee ne ee een ne ee een ee ere 106 Fg dle OMA sce E A dsc cc bata dats ceeccth cucpcestbancn eachiessdecaaieeaseeteinntaadaceeatiesasstananeds 106 21 4 Moving a specified ortholog group to the center of the SCreennuucece eee cece teers 107 21 5 Displaying gene information in a VOW SOU ccc ccc sede ceedch se acacsbetacedlacasincccpsetacacctetacedlarasbany 107 Lro Oane bale ONE eee Reece eee ene are er tea aCe Des one ee nt N epee rev em re are AT CeeeeertT ra 107 21 1 Recovering the OREN cca ai iaaa eA A sesh eis gcc EEA AKA AA AAN 107 27 8 Display Nondisplay of SPEC le Sia aniisawoaltietenriensedndenanemniauanaiienaeninmndnnetoe 108 21 9 Changing the display order of species aii craia tice tee siice stented een deceeecastenalabes EnciaeiMtcaslqcasiees lace tna cieattoe 109 27 10 Display Nondisplay of genes or ortholog lIN S wo ceceesesesessesecesecescessveseeesesveveveveseseetevveneneeeetanens 109 21 11 Changing the display style of species NAMES ou eee ese cceeeee cee ceeceeessesseeeesesseeeesesseuseveeenseneneens 110 27 12 Display
58. date function of the RECOG Client the gene information chromosome information Taxonomy Tree information and Function Category information can be updated 28 1 Updating the Taxonomy Tree based on the update notice If any gene information provided by the RECOG server is updated the icon is displayed on the lower right of the screen To display the update notice click the icon To update the Taxonomy Tree data on the All tab click the Update taxonomy only button in the notice message Ed Infor mation New gene data 2008 12 24 is released Inthe future this message should not be displayed Update taxonomy only Tf In the future this message should not be displayed is checked and the Close button is clicked no update notices will be displayed thereafter To display update notices again click aa Option in the Toolbox check Update information is regularly checked on the General tab on the Option screen and click the Apply button Taxonomy Tree PPM Function Category Color Neighbor Clustering Multiple Alignment _ Tree General Update V Updated information is regularly checked 115 RECOG Client User s Manual 28 2 Updating gene information through Update Data The RECOG Client can download data from the RECOG server This function is used to update the RECOG Client data when the RECOG server data have been updated 1 To display the Update data screen
59. ded 66 19 Enab Disable COnditioNS aesrespaiianio piin atts eee erence ee rete 67 130 Ramoval ol condition sosie a A 67 16 Filtering by Gene Count Species Count in the Phylogenetic Patterns cccccsssssccecesesseseeeseeseeens 69 10i cette the conditio sae ener a eee one ne en Pf eens tv err eee ve er PErErEN eT eTe nT 69 16 2 Enable Disable Conditions ccccccsssscssessssessesesessescssssssssssssssssessescssssessssessescssssesnsanessenesesceassneseeseseeseseesensens 69 iie Fk A haad SEA 70 e e n a S E a A E O 70 EEE crs el Ws E E OA AA AE O OAE N EAA AAA A A A AE E E EA eee 72 17a Redisplayine the Search results ee ements Pt Pee Rn 14 17 4 Enable Disable filter settings by the search results eceecsccceseseseccsccesessssscevsveveresssseseveneseeees 14 17 5 Enable Disable color settings by the search results eecccccsesesesescecesecessssseecsveveresesseeevareneeees 14 18 Changing the Display Order of Species or Display Nondisplay Status of Species c eee 75 RECOG Client User s Manual 18 1 Changing the order of display of SCC Saigo cee clecatcee testes cen ticuelecsti ce cteastl aa sieetitaclacaiimaloeatileata 715 18 2 Setting the display nondisplay Of SPECIES eeccesecesesesessssssescsessecsccesescecevavavecusevavaveseusseevavavveneseees 75 18 3 Adding species to be displayed jie cst eas icsccccnacusicscacestieatnnarnienakisina acesaasaindtunmcdeintebeessbusesetsieatianestnntateet 75 18 4 Removing displayed S
60. display the selected species on the PPM select the species on the Taxonomy Tree on the Selected tab click the right mouse button and click Show organism columns 18 4 Removing displayed species 1 Select species in the Organism Column on the control panel click the right mouse button and click Delete organism columns When the warning message is dislayed click the OK button 79 RECOG Client User s Manual 19 List of Genes A list of genes of the selected species is displayed be Taxonomy b Pp Genome Map b Gene order on bat Sort by gene properties tl Gene Ligt ASS Oromis Looto Genshime Accession teomaro Stet sca Cando co Pert 18352 esa ash kos booa poa 1300 Ceda co Oe ss a mal fos ana prae aie 13 420 20010 13 lt OS j 0260005 1 100 Cotter co 4 2033 21 612 626 000 Cebser co Pert 19 1 Displaying the list of genes 1 To display the Gene List screen select the species on the Taxonomy Tree on the Selected tab click the right mouse button and click Gene List on the pop up menu You can also click the right mouse button on an abbreviated species name in the header row of the PPM table to open the Gene List screen 19 2 Sorting the list of genes 1 To sort the gene properties in the ascending desceding order and display the gene property values click the gene property name on the Gene List screen 19
61. displayed il s0 sto_ST2096 ecj_JW2884 hal YNGOB 3G nph_NP2 104 sai_SACI_0062 sso_SS02266 sto_ST2096 ecj_JW2884 hal VNGOB 3G nph_NP2 104 sai_SACI_0062 sso_SS02266 sto_ST2096 ecj_JW2004 hal NGOB 3G nph_NP2 104 sai_SACI_0062 sso_SS02266 sto_ST2096 ecj_JW2884 QIASL RIRARODAAY AALNAL HAAGQUN NLLAAAVNAARYRA LG ISDALEYAFD WS EDSTRNYRCL YAK GLDGHDRG MWGMS TEGEQRT IRCLYAK YGLDGHDRG MKRIK LYAKLGLDGHDRG MMITTRRIKYIVAKLGLDGHDRG MSORRIKYLYARLGLDGHDRG RY LYPSOCYTGYIAQS HOS RSAS FDATYAQT gt QFLADNGRRPRIL TAK MGQDGHDRG ODDS RR AHYI TRAFRDAGFEYIYSGLHKAPDE IYQAAVOQ DYDYLGISTILSGAHNTLYPKITCGLA AHY IARAFRDAGFEYTYSGLHNSPDE IVOAAVOEDYDYLGISILSGAHOTLYPK ILDGLK ARVVARALKDAGH YYY TGLROTPEQIVKAAIQEDVDVIGYSILSGAHIELISMLYKEMK ARYYARALKDAGH VYY TGLROTPEQIVRAALQEDADVIGISILSGAHLELIPKYYE IMK AKYIARALKDAGMEYYYTGLROTPEQIVKSAIQEDYDVIGISILSGAHLELYPYVYNLMR AKVIASAYSDLGFOYDLSPMFSTPEE IARLAYENDVHVYGASSLAAGHK TLIPELYEALK Oe OE BOEID I D DRIDE I Bee RDE E EI E RIL II l EYDAAEDTLYIYGGI IPDEDRADLEAAGYDAIFGPGTPNADTISFIESNAPHRD EYDAFEDTLYITGGI IPDEDHDELYDAGYDE IFGPGASHEETITFYRENAFER D KKLNOYGLYYGGYIPPODIPALKOLGYDEYFLPGSSLKEITEKIIKYASDKRGLSFEP Q NGLNOYGLIYGGYIPPEDIKKLKEMGYDEYVFLPGSSLKEIVEKYKEYAREKRGISYE E KGLNOYYLYYGGYIPPADIPKLKEMGYDEYFLPGSSLKEYVEKITKAVETKRGIKIA K WGREDICYVAGGYIPPODYAFLOERGYAAI YGPGTPMLOSYRDYLNLISQHHO DE O ILOEEDEE DE E WE II ELI I 84 RECOG Client User s Manual 22 2 Changin
62. dow consists of the following components 5 2 Window header 5 3 Menu bar 5 4 Toolbox 5 5 Zooming scale bars 5 6 Taxonomy Tree 5 7 Phylogenetic Pattern Map PPM 5 8 Info tab 5 9 Histogram tab 5 10 Status bar 14 RECOG Client User s Manual 5 2 Window header The RECOG Client version name of the current project and name of the DomClust result file are displayed ba RECOG version 1 0 0 default cluster sample File View Search Run Option PS EI ona i e AWN eee ee r r 5 3 Menu bar 5 3 1 File menu View Tool Run Opti New Change Server b al Open file Open Project r ja Save Cluster file Import r 2 Export Genome Mapping gt Page setup pa Update Data F Exit New New Analysis The currently displayed analysis is cleared New Project A new project is created Change Server RECOG server The RECOG server to be used for analysis is specified Server List The list of registered RECOG servers is displayed Open file Analysis result files including DomClust result files are opened Open Project Project An existing project is opened 15 RECOG Client User s Manual Save Cluster file Import Export Genome Mapping Page setup Update Data Exit Soe Aggregate Mode Disaggregate Mode Cluster Mode Sub cluster Mode Expand Taxonomy Tree Collapse Taxonomy Tree Select all clusters on PPM Project List The list of existing pr
63. e Disable The same operation can be carried out by checking unchecking Display only matched clusters on the Keyword Search Result screen 17 5 Enable Disable color settings by the search results Select Color Keyword Search on the control panel click the right mouse button and click Enable Disable The same operation can be carried out by checking unchecking Highlight matched clusters on the Keyword Search Result screen 74 RECOG Client User s Manual 18 Changing the Display Order of Species or Display Nondisplay Status of Species In the Organism Column on the control panel the order of species displayed on the PPM can be changed or the display nondisplay of species can be set Control Sp Group Fitter Organism Column IN Bacillus cereus AH187 IN Bacillus cereus 4H620 IN Bacillus cereus ATCC 10987 IN Bacillus cereus ATCC 14579 IN Bacillus cereus B4264 18 1 Changing the order of display of species 1 To change the order of display of species drag the species in the Organism Column on the control panel to the destination On the PPM only the species displayed on the Organism Column are displayed 18 2 Setting the display nondisplay of species 1 Double click the species in the Organism Column on the control panel You can also click the right mouse button on the species and choose Show Hide to set the display nondisplay modes 18 3 Adding species to be displayed 1 To
64. e column on the right of the species to be set as the reference genome Click the Apply button 100 RECOG Client User s Manual d Gore Genome Alignment B amyloiquefaciens FZB42 B arthracis Ames Ancestor A2 B anthracis Ames B anthracis Sterne B cereus ATCC 10987 B cereus ATCC 14579 Up I Down Abbrevistion Cluster ID Presentative gene nome of the cluster Gene name of the reference genome Display Nondisplay of species To display the screen for changing the Core Genome Alignment view click View View Change on the Core Genome Alignment screen To display species select the species in the Candidate column and click the gt gt button To hide species select the species in the Target column and click the lt lt button Click the Apply button Changing the display order of species To display the screen for changing the Core Genome Alignment view click View View Change on the Core Genome Alignment screen To change the display order of species select the species in the Target column on the screen for changing the Core Genome Alignment view and click the Up or Down button Click the Apply button 101 RECOG Client User s Manual 26 10 Resetting the window size 1 To display the screen for changing the Core Genome Alignment view click View View Change on the Core Genome Alignment screen 2 To reset the window size of the neighborhood r
65. e for use in analysis Ifthe Save column is checked the entered name Ifthe Save column is unchecked Phylogenetic Pattern Coefficient 33 5 Uses of the results of the phylogenetic pattern similarity search The results of the phylogenetic pattern search can be used in the following functions Display on the cluster header PPM sorting see 13 PPM Sort 138 RECOG Client User s Manual Filtering by keyword search see 17 Keyword Search Color setting by properties see 12 Color Display by Properties 33 6 Removing the phylogenetic pattern similarity search 1 The coefficient of correlation saved to a file upon checking the Save column can be removed on the Cluster property tab on the Gene property Cluster property screen For the method of removal refer to 29 2 Referencing a list of gene cluster properties 139 RECOG Client User s Manual 34 Downloading the sequence information Download the protein DNA sequences of the genes contained in the cluster selected on the PPM 34 1 Downloading the sequence information 1 Select a cluster on the PPM 2 Click the right mouse button and choose Download sequence The Download sequence screen is displayed Download sequence Additional bases upstrearn dovenstrearm Split in delimiter Target genes All genes onthe cluster table Genes include the select clus
66. e sets only Project registration destination project Cluster sets only DomClust File registration destination DomClust result file name Cluster sets only Cluster Count registration destination DomClust result file name Cluster sets only Gl Gene set Cluster set 3 To register edit or remove a gene cluster set click the Add Edit or Delete button respectively 126 RECOG Client User s Manual 31 Combined Set A combined set consisting of multiple gene cluster sets can be created The combined set can be utilized for coloring filtering etc based on the results of set operations using multiple sets 31 1 Registering a combined set 1 Registering a combined set of gene sets Select gene sets in Gene Set on the set control panel to display the Gene set combination screen click the right mouse button and click New gene set combination Registering a combined set of cluster sets select cluster sets in Cluster Set on the set control panel to display the Cluster set combination screen click the right mouse button and click New cluster set combination ta Gene set conbmation Condition Test gene set 1 amp Test gene set 2 amp Test gene Test gene set 1 amp Test gene set 2 Test gene set 2 amp Test gene set 3 Test gene set 1 amp Test gene set 3 Down 2 On the Gene Cluster set combination screen specify the gene cluster set names and
67. ecked registration is made upon overwriting the gene cluster set of the same name if such a set exists Registered gene cluster sets are displayed in Gene Set Cluster Set on the set control panel 123 RECOG Client User s Manual 30 2 Outputting a gene cluster set to a file 1 To display the Export gene cluster set screen select gene cluster set in Gene Set Cluster Set on the set control panel click the right mouse button and click Export gene cluster set 2 On the Export gene cluster set screen select the file name to be saved and click the OK button 30 3 Editing a gene cluster set removing genes 1 To display the Edit gene cluster set screen select a gene cluster set in Gene Set Cluster Set on the set control panel click the right mouse button and click Edit gene cluster set 2 On the Edit gene cluster set screen change the name destination for registration only for gene sets or remove a gene cluster To output the list of genes clusters registered as a gene cluster set to a file click the Export button 3 On the Edit gene cluster set screen click the Apply button td Edit gene set S CB4264_A4710 lacetyLCoA carboxylase cosets knal bee i lt tsst iw of carboxylase Serouteeneters ber BCAH18 44726 of carboxylase Itranster bou CAHE20 4715 Cod carboxylase carboocyl transfer oh ss 0B2173 acety CoA carboxylase carhoxyitransfera 124 RECOG Client Use
68. ed See 31 Combined sets Species sets are displayed See 32 Species sets 45 RECOG Client User s Manual 11 Display and Operation of the Phylogenetic Pattern Map On the Phylogenetic Pattern Map PPM the appearance patterns of species belonging to a cluster are displayed 11 1 Display of the locus tags of genes belonging to a cell The locus tags of genes belonging to a cell are displayed on the cell If the cell region is narrow the gene count is displayed The display can be switched on off as follows 1 Click Option in the Toolbox to display the Option screen Click the PPM tab on the Option screen 2 Check Display gene names or the number of genes on the PPM tab 3 Click the Apply button 11 2 Display of the cluster property on the cluster header The value of the property corresponding to the cluster is displayed in the display area cluster header on both sides of the PPM To change the displayed property do the following 1 On the cluster header click the right mouse button and on the menu PPM Label click the property to be displayed this displays the property value on the cluster header Cluster ID The homology cluster ID cluster ID and sub cluster ID are displayed Gene name The typical gene name of the cluster and the typical gene name of the sub cluster are displayed default value Cluster score The cluster score and sub cluster score are displayed
69. ed ortholog group is relocated to the center of the screen 27 5 Displaying gene information in a browser 27 0 Click aL Show the gene information at clicking gene in the Toolbox on the Genome Comparison Viewer screen Upon double clicking in this state the information on the default external resource set in 35 External Resource URL Management is displayed in a browser To display the information on the external resource in a browser click the right mouse button and click the displayed external resource URL Saving the origin To save the current origin center point click View Save Origin on the Genome Comparison Viewer screen 27 7 Recovering the origin To relocate the genome map with the origin saved immediately before as the center point I click ie Recover Origin in the Toolbox on the Genome Comparison Viewer screen 107 RECOG Client User s Manual 27 8 Display Nondisplay of species Specify the species set to be displayed on the Genome Comparison Viewer screen 1 Click View View Change on the Genome Comparison Viewer screen The screen for changing the display of the Genome Comparison Viewer screen is displayed Click the View tab on the screen for changing the display of the Genome Comparison Viewer screen 2 To display species select the species in the Candidate column and click the gt gt button 3 To hide species select the species in the Target column and c
70. ee eet 13 Display and Operation of the RECOG Main Window uu ccc seeceecesceeessesseseeseeseveeseeseuseneeeensenenss 14 FTN Pee gt N EN deen eee eee ee ne eee eee ee ee eee ee 14 Se Ue NN asses ce cee AA NE A baat A cect eee eee 15 SU A ace eens reese E E sese vecencseoeeee eerereeee tie 15 aTe e S a Sean ae eee EA ee ENE EA eae nae A E A anne Ao me nner E ne A ne ae 18 Be Ot 0 ON racine eden eeee science eo nere nee 19 ig Me Faas rset E gleoimsceen mutants ist ecdoimtaeedam tiesto 19 5 7 Phylogenetic Pattern Map PPM oonicccccssssssssssssscsssssssssesstsessesssesatssstsesessnsaeensaesnseen 20 Bs NRE Or NN EE EEEE A cast E ccc N cee E E EEN E ste E EEE E E E AE EAN 21 PEE e E E E EE E E ES N E E E EA EE AAA E E OAA NS P E AE 23 ER Se aT cy AEA OE E AA E A O A A N O A E N E AN E 24 Project Creation and EdItINE senrose aia E aa 25 0 CGreatonof a new Proj tt ecas aaa a O 25 EARE a EE lt N EIES ALEA AE P VE AEE EEE E A EEEE AE N EEA AE EE EE E T 26 6 3 Reference to a list of registered ProjeCts oo ec cece cece ssscsceeeessssessesesseesesseseesessesseseuseuseseusessevessenseeees 26 04 Froect reci ccc eects ec E E 21 RECOG Client User s Manual 0 9 Froject normato edine ae eee md et ne a te ne 2 ON essa eee cee eget case eset cece asec scatter TAE OA 28 Switching the i OP sisiane aiaiai idiniin 29 7 1 Checking the RECOG Server USE cece ceccseecscesceseeceecessesessessesessessessevseeesseusesesseusesesseusessaveneensenees 29 7 2
71. eeter rtm 36 9 3 Display of the DomClust analysis FES OILS sia cecusissscactiivazcateansicrasesinrerasavecaneadoinesenasiaternastvooaniadineeiuasiiecens 39 9 4 Display of the DomClust analysis result properties cece ce ceeceseeceecesesessevsesesseseuseesnses 40 9 5 Storage of the DomClust analysis results ascii secs ccchcscshcacescenciceinetciondiaciavndcventineedadcenils 41 Control Panel and Set Management Panel ccc cess ceseesesceseesescesseesesessessessesesseusesesseusevenseusevseeneess 42 10 1 Display on the control eect secre n sc cca cteete vet eweoat cman ectearc act aeta const encematsdaseenteeeeeeceeond 42 10 2 Controli panel operatio meee een etree Na ten ty ean nn nr pe SO ev ee ne Pv Pe eT 43 10 3 Display of the SEE management panel caiicccisscceccscceccicescetctendlecsectcisceceiceusckaveioncemsustanideos doatebaatinnaveneeuades 44 10 4 Operation of the set management Panel uu eee ese eee seecesceseeseesesseseeseseseeseesessessessseusevensessensees 45 Display and Operation of the Phylogenetic Pattern Map ccc cescecesescescesessessevessesseeseneeeens 46 11 1 Display of the locus tags of genes belonging to a Cello csceceesceeceeeeseeseeeeseeseneeeeeeeees 46 11 2 Display of the cluster property on the cluster header eee cece ceeeceeceeeeseeseeeeseeseneeeeeeeees 46 11 3 Display Nondisplay of the homology cluster Meader ceecscccssesesescscesesesessseecsvavesesssseeeveneseeees 41 11 4 Species color setting o
72. elation set the value in the Window Size section 3 Click the Apply button 26 11 Changing the display style of species names 1 To display the screen for changing the Core Genome Alignment view click View View Change on the Core Genome Alignment screen 2 Select the display style in the Organism column on the screen for changing the Core Genome Alignment view Normal Species are displayed according to their official names Abbreviation Species are displayed according to their abbreviated names Show Strain If this is checked the strains are displayed 26 12 Changing the ortholog group labels 1 Click View View Change on the Core Genome Alignment screen The Core Genome Alignment view is displayed 2 Specify the items to be displayed as labels for the ortholog group in the Label section on the screen for changing the Core Genome Alignment view Cluster ID The cluster ID corresponding to the ortholog group is displayed Representative gene name of the cluster The representative gene name of the cluster corresponding to the ortholog group is displayed Gene name of the reference genome The gene name of the reference genome is displayed If gene name is undefined in that 102 RECOG Client User s Manual genome the Locus Tag is displayed If these items are specified the gene name display column on the PPM is switched synchronously 26 13 Zoom 1 To zoom in zoom o
73. elected Clustering j cr ey root 6 C Bacteria 6 Bacillales 6 of C Bacillaceae 6 oe ee acl IN Bacillus cereus 4H18 IN Bacillus cereus 4Hb20 brB n 87 A008 8 h cereus ATCC 10987 pe IN Bacillus cereus ATCC 14579 eck IN B p eae Taxonomy All Sp Group b Any New P Genome Map gt Any Add gt Gene List None Control Gene order on beb Cancel Bacillaceae 15 4 Chang ng the names of the Any conditions On the control panel select Filter Taxonomy Filter name of Any condition click the right mouse button and click Rename to display the Rename screen Name Bacillaceae On the Rename screen edit the name and click the Apply button 65 RECOG Client User s Manual 15 5 Changing the threshold value of the Any conditions 15 6 On the control panel select Filter Taxonomy Filter Name of Any condition to display the conditions for phylogenetic pattern filtering From among the conditions for phylogenetic pattern filtering select the Any condition click the right mouse button and click Any Threshold Edit to display the Any Threshold screen On the Any Threshold screen specify the Any conditions For details refer to Item 3 of 15 2 Setting the Any conditions To specify the Any conditions more easily select and click Any click the right mouse button and click Tax
74. elected color pattern upward downward 94 RECOG Client User s Manual 25 Species Groups Multiple species closely related to each other can be registered as a species group The species groups registered here can be used in the analysis such as the CoreAligner program 25 1 Displaying species groups 1 To display the species groups set in the lower view of the Taxonomy Tree click the Sp Group button in the upper view of the Taxonomy Tree on the Selected tab A Selected Clustering Fiter Sp Group O Select It Bocus omylotquetaciens FI642 In Bacius artivactt Sterne IR Gocis cereus ATCC 10987 In Bacus c r ut ATCC 14579 th Bactius cereus ES In Bacius cereus NYH 391 96 IE Bacius thuringiensis serovar korubion 97 27 IN Bacius thuringiensis Al Hakam IE Bacillus clousd KSM K16 cre Mee Me Vafethmene AAAF Sacilus amyhiquetaciens FZB42 Socilus cereus ATCC 10997 25 2 Registration of species groups 1 To create a new species group with a specified set of species select the species on the Taxonomy Tree in the upper view of the Selected tab click the right mouse button and choose Sp Group New Group The species group is displayed in the lower view Al Selected Clustering Fiter Sp Group O Select An Selected Chasterina Fiter Sp Group Select ik Bocus omyiotquetociens FZG42 in Bacdus artivacit Sterne IE Bacillus cereus ATCC 10987 In Bacius cereus ATCC 14579
75. ene count gt 2 Base Color Phylogenetic Pattern 2 Control panel 10 1 Display on the control panel Click the Selected tab on the right side of the screen and click the downward Control button to display the control panel 42 Sp Group Gene Set Test gene set 1 4 Test gene set 2 3 Test gene set 3 4 Gene Set Conbination Gene Conbination 1 Cluster Set Test cluster set 11 Test cluster set 2 1 Test cluster set 3 1 Cluster Set Conbination Cluster Conbination 1 Organism Set CH Organism Set 1 Bacillus cereus 4H187 Bacillus cereus AH820 Bacillus cereus ATCC 10987 Organism Set 2 Set management panel RECOG Client User s Manual 10 2 Control panel operation 10 2 1 Filter settings Filter Filter refers to the conditions for selecting the row cluster that is displayed on the PPM In the Filter folder on the control panel the filter conditions that are currently applied to the PPM are displayed Only those clusters that meet all the filter conditions are displayed on the PPM Click Enable Disable to enable or disable the filter settings The following filter conditions can be specified Taxonomy Filter Phylogenetic pattern filtering See 15 Taxonomy Filtering Gene Organism Count Filter Filtering by gene count species count See 16 Filtering by Gene Count Species Count in the Phylogenetic Patterns Keyword Search Filtering by key
76. es is displayed Cluster Property List Gene Set Cluster Set List The list of registered gene sets cluster sets is displayed Properties The properties of the displayed analysis results are displayed 5 4 Toolbox Ub a RO CRE p v ist The Toolbox can be moved by dragging and dropping the left side of the Toolbox with the mouse To return the Toolbox to its original position click the Close button on the upper right of the Toolbox Open file Save Cluster File Import DomClust file Export Aggregate Mode Disaggregate Mode Cluster Mode Sub Cluster Mode Expand Collapse Taxonomy Tree Color genes by properties Histogram Keyword Search Ortholog Clustering DomClust Phylogenetic pattern clustering PhyloPatClust Core Genome Alignment CoreAligner 18 RECOG Client User s Manual mg aH Neighboring Clusters Wd Option 5 5 Zooming scale bars Each zooming scale bar expands or contracts the horizontal vertical size of the PPM Horizontal Zoom _ 1L Vertical Zoom scale bar Vertical Zoom The longitudinal size of the PPM cell is expanded or contracted by sliding the scale bar laterally Horizontal Zoom scale bar The transverse size of the PPM cell is expanded or contracted by sliding the scale bar laterally 5 6 Taxonomy Tree The Taxonomy Tree displays the taxonomic tree of the given species 1 All tab for selecting the species to be anal
77. etic pattern can be displayed by graphs or the numerical data of the specified gene properties can be displayed by bar graphs 23 1 Function category frequency graphs In the Disaggregate Mode the frequency of each function category in the same phylogenetic pattern is displayed in a graph on the Histogram tab wh Moye wW i 71 5 m i 23 2 Displaying a numerical data graph a description or the function category In the Disaggregate Mode a graph of numerical gene property values or the description and the function category of each cluster is displayed on the Histogram tab 1 To display the Histogram screen click Histogram in the Toolbox be Histogram Organism E cereus 4H1S 7 Property Ist art Difference Organism 1 5 cereus AH157 L Organism 2 E cereus AH320 Property V Show value RECOG Client User s Manual 2 Specify the graph to be displayed on the Histogram tab Description Function Category The description of the cluster is displayed with the color of the function category of the cluster in the background Pyridonine bloastAhes s erotcin Glycerate kinase Cid Value The specified numerical property data are displayed by a bar graph Cluster property data or gene property data of a specified species can be displayed reo Hoty ga gtn oih 7500 GKOSSS Difference The difference in the nume
78. f the Locus Tag Click View View Change on the Genome Comparison Viewer screen Click the View tab on the screen for changing the display style of the Genome Comparison Viewer screen To display the Locus Tag on the genome map check Show in the Locus Tag column on the screen for changing the display style of the Genome Comparison Viewer screen In the Row count specify the number of rows for displaying the Locus Tag If multiple rows are specified their space is used so that names do not overlap each other To hide the Locus Tag on the genome map uncheck Show in the Locus Tag column If 0 is specified in the Row count the distance between genomes takes its minimum value and the Locus Tag is not displayed regardless of whether Show is checked or unchecked Click the Apply button 27 13 Color setting The color can be set based on the gene position on the reference genome or it can be set on the Color tab on the control panel k Click View View Change on the Genome Comparison Viewer screen Click the Color tab on the screen for changing the display of the Genome Comparison Viewer screen On the Color tab set the colors for genes and ortholog lines Reference genome Core genes are colored with color gradations from green to red based on the gene positions on the reference genome Non Core genes and RNA are colored in grey and deep blue respectively Use the color of the control tree For colori
79. g species where each row represents ortholog group and each column represents species In RECOG an ortholog table is represented 148 RECOG Client User s Manual as a phylogenetic pattern map PPM Outgroup The set of control species in phylogenetic analysis which are located outside of the ingroup on the phylogenetic tree In the DomClust analysis outgroup species is specified as the group of species which do not belong to the ingroup P Phylogenetic pattern In a strict sense a binary vector that indicates the presence 1 or absence 0 of a gene for each species defined for each orthologous group In a more broad sense a numeric vector that indicates some gene property value of each species Phylogenetic Pattern Map PPM A matrix that shows the presence or absence of species based on the DomClust analysis results R RECOG http mbgd genome ad jp RECOG Research Environment for Comparative Genomics A client server type software program that is a comparative genome workbench for conducting various comparative analyses based on DomClust analysis results RECOG server The server that conducts the DomClust analysis and CoreAligner analysis and provides gene information in concert with the RECOG Client Regional Genome Map RGM A genome map for ortholog comparison I Taxonomy Tree A phylogenetic species classification in tree form 149
80. g the colors of the amino acid letter strings ius Color Settings x 1 Click the Color Setting button on the Multiple Alignment screen to display Cystein the Color Setting screen Aspartic Acid Glu Glutamic Acid Phenylalanine Glycine His Histidine le Isoleucine Lysine Leu Leucine 2 On the Color Setting screen you can specify the colors of the amino acid letter strings Met Methyonine Asn Asparagine a A D E _ M N a a Glutamine Apply Restore Close f 22 3 Displaying the phylogenetic tree 1 To display the Phylogenetic Tree screen click Clustal Tree on the Multiple Alignment screen 2 To change the parameters used in the creation of the phylogenetic tree click Ve Option in the Toolbox Specify the parameters on the Tree tab on the Option screen Taxonomy Tree PPM Function Category Color Neighboring Clusters Muttiple Alignment Tree General KMURA iON v TOSSGAPS ON vl OUTPUTTREE phijip v pootstRae on Oof COUNT 1000 seo 111 85 RECOG Client User s Manual ta Phylogenetic Window 0 9 121 File View Option Settines SEX S Bw 1222403069650 phb bt I _BALH_3793 bez 8CZK3938 0 1 bce _BC4134 btk _BT9727_3927 bat _BAS4089 bea BCE 4258 bey BCERSB_2878 zka_GK2400 ztn_GING_2331 bha_BH2788 bl d_BL102606 het _ABC2469 7 PUN ry pu BPUM 2167 022680 oih_OB 1886 638 RE xe OND os 3 On the Phylogenetic
81. gate Mode oe Pe re ee EET aT 13 3 S0rt based on I 96 61 gl lt lt sirnaan nO AD 58 13 4 Display of the sort CANIS cca cs ced act ceca ctn arcades had alse eee dec ndonwossececulietaluaetaonte 59 14 Phylogenetic Pattern Clustering PhyloPatClust c cecssesssscsscsssesesessesessesesssesessesesecseseserereesevatsesersesecees 60 14 1 Execution of PUI IOP BSE sccsiticsnsininsrcenrinsiestcasionmnssrorasintcstaitin iestadenontsdun E eai ianei 60 14 2 Operation of the clustering tree aac reas scesticcaca bisa snadendeecavead iuctniphecceneacsescanetbimaimcedtaetancstpinaeddetiinimueaarelibe 61 US mm 01g S106 Weg Loc a lt eee eee ee ee een oe te eT ene ene een Pn 62 15 1 Displaying the taxonomy filtering conditions iaceisiiccccscdccccasdsccccsosnasliescnscasscssscnsoncasaeseamsbarssbscseanmenecnance 62 15 2 Setting the Al conditions sccessescasscactcsensttvesasccsisoasadsincessicsbuedstscexncanin avansisl deunwsaiveueuaseceuseisncouemesnnnsesaeas 63 15 3 Setting the Any COnCICIONS ccccccsssecsscsesssssesesseesecsecsecsessessecsessesatsaesucsussecsecsessessessessesatsatsessacsessessecsesees 63 15 4 Changing the names of the Any conditions ccscsssssssecsesssssessesecsessecsecsessessessessesetsatsecsecsessessesseeees 65 15 5 Changing the threshold value of the Any conditions cccccsessssscsessessesecsesecsesseseesecsesseseesecsecseees 66 15 6 Setting the None conditions seeen a ngs A EA aa AE scales cee
82. genes 27 15 Changing the display style of the scale marks Scale Relative postion from center Position of reference genome 1 Click View View Change on the Genome Comparison Viewer screen 2 On the Scale tab set the display style of the scale marks Relative position from center The relative position from the center is displayed on the scale marks 113 RECOG Client User s Manual Position of reference genome The position based on the coordinates of the reference genome is displayed on the scale marks 27 16 Printing Genome Comparison Viewer Preview O Specification 100 lt Page setting 1 Click File Preview on the Genome Comparison Viewer screen The Genome Comparison Viewer Preview screen is displayed 2 On the Genome Comparison Viewer Preview screen the following settings are possible Zoom Specify the image magnification If Auto is specified the image magnification is adjusted so that the image fits onto a single sheet of paper Page settings Specify the paper size etc 3 Click the Apply button The print setting screen is displayed Printing is carried out in accordance with the screen display To directly print without displaying the Genome Comparison Preview screen click File Print on the Genome Comparison Viewer screen 114 RECOG Client User s Manual 28 Updating the Gene Information Using the gene information up
83. ging to A and B that are adjacent to each other and Faaji and Fagj2 are parameters satisfying 0 lt Faaji lt aaj lt 1 Coverage ratio fagz for absorbing See above Note that this parameter is not effective if Fadj2 lt aaj adjacent small clusters Use domclust dump If this is checked the DomClust analysis is conducted using the cache for previous DomClust analysis results This shortens the processing time of the analysis 146 RECOG Client User s Manual 37 Glossary A Aggregation Integration of clusters of the same phylogenetic pattern into a single row in the phylogenetic pattern map C Cell A square corresponding to a species belonging to an ortholog group on the PPM CoreAligner http mbgd genome ad jp CoreAligner A software program for creating a core structure based on the preservation of gene alignment sequences between affinity genomes Circular Genome Map CGM A gene map on which genes etc are drawn in a circle ClustalW A software program for performing the Multiple Alignment Cluster A group of genes grouped together based on DomClust analysis results Cluster ID A unique ID given to each cluster COG http www ncbi nlm nih gov COG Clusters of Orthologous Groups of proteins COGs D DomClust http mbgd genome ad jp domclust Hierarchical clustering program for orthologous protein domain classification which is the standard method to construct ortholog groups in RECOG E Extra T
84. he Genome Comparison Viewer screen For changing the display area there are two modes as shown below The two modes can be switched by clicking the relevant button in the Toolbox t Simple Mode In this mode the display area is moved within a certain interval without adjusting the gene display position o I Adjust Mode In this mode after changing the view area the display is made upon relocating so that the genes belonging to the ortholog group that contains the gene near the center of the view area on the reference genome align or stand in a straight line Also regarding the orientation of the genes the display is made upon making the gene orientation uniform according to the settings described in 27 14 Automatic correction of gene orientation 27 3 Zooming 1 To zoom in zoom out on the display area click Toolbox on the Genome Comparison Viewer screen respectively 2 If the zooming in exceeds a certain scale the screen automatically switches to the detailed 106 RECOG Client User s Manual gene view 27 4 Moving a specified ortholog group to the center of the screen In normal mode the mode without the operation set out in 26 5 below upon double clicking on the genes belonging to the ortholog group on the Genome Comparison Viewer screen the double clicked ortholog group moves to the center of the screen Also on the Core Genome Alignment screen as well the click
85. in the same cluster lt Specified value Calculate by applying a specified value 137 RECOG Client User s Manual Representative value of multiple gene property values Specify the method of determining the representative value when multiple values are defined for a gene lt gt lt gt lt gt lt gt Min The minimum value among multiple values is used Max The maximum value among multiple values is used Median The median among multiple values is used Average The mean value of multiple values is used Representative value of multiple genes in one cell Specify the method of determining the representative value when there are multiple genes in a cell lt gt lt gt lt gt lt gt Min The minimum value among multiple genes is used Max The maximum value among multiple genes is used Median The median among multiple genes is used Average The mean value of the gene properties of multiple genes is used 4 To calculate the dissimilarity of the specified pattern with each cluster click the Apply button after specifying the conditions After the phylogenetic pattern similarity search is completed the calculated dissimilarity value is displayed on the label on the side of the PPM Also if Sort by the calculated result is checked the PPM is sorted based on the value of dissimilarity The dissimilarity value is registered as a cluster property under the following nam
86. ing two most similar sequences or clusters the algorithm searches for another sequence S3 that matches one of the merged sequences S1 in the region outside the alignment between the merged sequences The algorithm splits the sequence S1 if such a sequence S3 is found and the alignment between S1 and S3 satisfies the coverage condition specified by this parameter and score condition specified by the next parameter Raise this parameter to avoid excessively short domains generated due to partial matches Cutoff score for the match between S1 and S3 described above to split the sequence The effect of this parameter is similar but possibly complementary to that of the previous parameter This option specifies which similarity or dissimilarity measure score or PAM for use in orthology identification or clustering Note that the scores depend on the alignment lengths while PAMs do not The bi directional best hit criterion i e gene pairs a b of genomes A and B such that a is the most similar gene to bin A and vice versa is a conventional approach for ortholog identification between two genomes The uni directional version 144 Cutoff ratio of the score against the best Score for missing relationships Clustering Mode Cutoff ratio of paralogs for tree splitting Phylogenetically related organisms Overlap ratio fag1 for merging RECOG Client User s Manual is also routinely used for predicting gene function
87. ions double click the Color column in the Condition column and modify it on the Color selection screen displayed 3 In the Filter Color setting column specify whether or not to apply a combined set to the color filter setting Filter and Color Register a combined set to add it as the condition for the color filter setting Color Register a combined set to add it as the condition for the color setting 128 RECOG Client User s Manual Filter Register a combined set to add it as the condition for the filter setting None Register only combined sets To display the combined conditions in Gene Set Combination Cluster Set Combination on the set control panel specify the conditions on the Gene Cluster set combination screen and click the Apply button If Filter and Color or Filter is specified in the Filter Color setting column the filter conditions are displayed in Filter Gene Set Filter Cluster Set Filter on the control panel If Filter and Color or Color is specified in the Filter Color setting column the filter conditions are displayed in Color Gene Set Cluster Set Filter on the control panel The specified filter settings and color settings are reflected on the PPM in the comparative genome map view etc An Selected Chictening I roet s E S Bacterias 5 E Bacitaies 5 9 Bacitacese 5 IN B c us cereus ANIET IN Bact cereus AH220 IN Bactazt c reus ATCC 10057 IM Bacthzt cere
88. is opened the default RECOG server that is set for the project conducts the analysis 7 1 Checking the RECOG server used 1 Click File Change Server to access the list of URL s of registered RECOG servers The server currently used for analysis is checked View Search Run Option New b TS see SS oe http mbed eenome ad jp J Open file R a server List Open Project Save hicter file 7 2 Switching the RECOG server 1 Click File Change Server and click the RECOG server to be used The RECOG server in use is Switched and the Taxonomy Tree on the All tab is updated using the data from the newly specified RECOG server Note When the DomClust analysis results are displayed the RECOG server cannot be switched Click File New New Analysis to clear the display and start a new analysis 7 3 Reference to the registered RECOG servers 1 Click File Change Server Server List to display the Server List screen A list of registered RECOG servers is displayed The RECOG server used for analysis is checked in the Select field 29 RECOG Client User s Manual Server List Name http mbgd genome ad jp http recog server ac jp O 7 4 Registering the RECOG server 1 Click File Change Server Server List to display the Server List screen 2 On the Server List screen click the Add button to display the New Server screen 3 On the New
89. ister Phylogenetic Pattern Bacillus cereus AH820 iO Bacillus cereus ATCC 10987 i000 2 On the Register Phylogenetic Pattern screen specify the profile name and weight for each species To change the weight select the species in the list of species on the lower right and specify the weight in the Setting Value column lt Value Specify the weight value lt Ignore Specify the species to be ignored in determining the coefficient of correlation 134 RECOG Client User s Manual After selection click the Set Value button You can change the weight using a species set To do so select the species set in the Species Set column above the list of species Upon selection the species contained in the species set are selected in the list of species Then set the weight of specified species in the Setting Value column 3 After specifying the conditions click the Apply button The profile is displayed in Phylogenetic Pattern on the control panel Control Fitter Organism Column Sort Color Phylogenetic Pattern Phylogenetic Pattern 2 Phylogenetic Pattern 1 Sp Group 33 2 Editing a profile 1 To display the Register phylogenetic Pattern screen select a profile in Phylogenetic Pattern on the control panel click the right mouse button and click Edit pattern 2 Edit the profile For the editing method refer to 33 1 Profile registration from a cluster 3 Af
90. kground color of a cell can be changed according to the gene count within the cell by setting a threshold value 1 Select Color Gene count on the control panel click the right mouse button and click Edit to display the PPM tab on the Option screen 2 On Background color cells containing inparalogs gt genes on the PPM tab specify 48 RECOG Client User s Manual the threshold gene count and the background color of the cell Click the Apply button to display the color setting condition on Color Gene count on the control panel To enable disable the color setting double click Color Gene count on the control panel 11 7 Color display corresponding to each functional category The color corresponding to the typical functional category of a cluster is displayed in the gene name display field l Click WA Option in the Toolbox to display the Option screen Click the Function Category Color tab on the Option screen 2 On the Function Category Color tab specify the functional category for drawing Taxonomy Tree PPM Function Category Color Neighbor Clustering Multiple Alignment Tree General Function Category MBGD v 1 Amino acid biosynthesis 1 1 Aromatic amino acid famity 1 2 Asportote famiy 1 3 Branched chain famity 1 4 Ghtamate family 15 Pyruvate family 15 Serine family 1 7 Histidine famiy S 2 Purines pyrividines nucleosides and nucleotides
91. l on the control panel and to display the relevant species names on the tree in light red asl Selected Gustering All Selected Clustering root 6 9 root 6 I E Bacteria 9 BacterialS S OY Soctiaies 6 A Bacillales 6 Bacifacene 6 9 Bacillaceae 6 IN Bacillus cereus 4H187 IN Bacillus cereus AH820 IN Bacillus cereus ATCC 10987 IN Bacillus cereus ATCC 14579 IN Bacillus cereus B4264 OUT Oceanobacillus iheyensis HTE831 IN IN Be Taxonomy ik Be Sp Group ik Be Genome Map our Ox Gene List Gene order on bcu 15 3 Setting the Any conditions 1 Select two or more species names on the Taxonomy Tree in the upper part of the Selected tab 2 Click the right mouse button and click Taxonomy Any New Setting to display the Any Threshold screen Any Threshold Name siete cle ot AN tanaan ctustering O Coun 1 less o 1 a Bact v or more 14 A 3 C Bacilses 6 oft So aa sac Percent C orless 0 IN Eachus careus AH167 IN Eactus cereus AH320 IN a A AL 10967 IN Bactus cereus ATCC 14579 A ormore 50 0 209 40 60 8 100 js fe Taxonomy a All Sp Group A fey New gt Setting Genome Map po ny Add gt For of Any Corxitions Gene List None One or more Gene order on bcb Cancel 20 or more Fitter a 40 or more Samm aego ee moreris ndh ener mre a OJAD FHH Neighboring Chisters_ SOK or m
92. le format output by clicking Export gene cluster set Ce Gene property format This is the file format described in 29 1 Registration of gene properties 121 RECOG Client User s Manual 2 Click File Import Gene set file and select the destination for registering the gene set Select from among the following Current Project project name Register the gene set so that it becomes available only in the current project or in the specified projects Global Register the gene set so that it becomes available in all projects Register gene set Name File Location Overwrite the gene set of the same name 3 The Register gene set screen opens To register the gene cluster set specify the set name gene cluster set file and the destination for saving and click the Apply button If Overwrite the gene cluster set of the same name is checked the registration is made upon overwriting the gene cluster set of the same name if such a set exists The registered gene cluster set is displayed in Gene Set Cluster Set on the set control panel 30 1 2 Registration from the cluster selected on the PPM 1 Select the cluster on the PPM 2 To open the Register gene cluster set screen click the right mouse button and click Create gene cluster set 3 To register the gene cluster set specify the set name and the destination for registration on the Register gene cluster
93. lick the lt lt button 4 Click the Apply button B cereus AH187 B cereus AH820 B cereus ATCC 10987 B cereus ATCC 14579 B cereus B4264 OUT Oheyensis HTESS1 OO000 8 Up Down Display elements Organism Morne V Core genes One Lines Universal Onity 1vs1 Onity Non Core genes V Unique Only Abbrevistion v Line Universal Only v 1vs1 Only Show Strain 108 RECOG Client User s Manual 27 9 Changing the display order of species 1 Click View View Change on the Genome Comparison Viewer screen The screen for changing the display of the Genome Comparison Viewer screen is displayed Click the View tab on the screen for changing the display of the Genome Comparison Viewer screen 2 To permute the species select the species in the Target column on the View tab and click the Up or Down button 3 Click the Apply button 27 10 Display Nondisplay of genes or ortholog lines 1 Click View View Change on the Genome Comparison Viewer screen Click the View tab on the screen for changing the display of the Genome Comparison Viewer screen 2 Inthe Display elements column on the View tab specify the display nondisplay of genes and the display nondisplay of the lines that represent ortholog relationships Genes and RNA display switching options Option Details Core genes The genes extracted by the CoreAligner analysis are called Core genes
94. ll If a cell contains multiple genes specify the method of determining the representative value for the sorting lt Min The minimum value among the multiple genes is used lt Max The maximum value among the multiple genes is used lt Median The median among the multiple genes is used lt Average The mean value among the multiple genes is used Only numerical type gene properties apply 3 After specifying the sort conditions click the Apply button to sort and display the phylogenetic patterns on the PPM according to the sort conditions 13 4 Display of the sort conditions The currently valid sort conditions are displayed in the Sort folder on the control panel Control Sp Group Fitter Organism Column q Category gene name Function Category MBGD Cluster Gene name Cluster Cluster ID Sub Cluster ID 59 RECOG Client User s Manual 14 Phylogenetic Pattern Clustering PhyloPatClust Upon the analysis of the phylogenetic pattern clustering PhyloPatClust each ortholog group is clustered based on the similarity of the phylogenetic patterns and sorted based on the results Also the clustering tree is displayed on the Clustering tab 14 1 Execution of PhyloPatClust 1 Glick Wee Phylogenetic pattern clustering PhyloPatClust in the Toolbox to display the Confirm screen 2 Specify the conditions on the Confirm screen El Confirm Q Phylogenetic Pattern
95. lobal uneditable System defined gene properties provided by the RECOG server They cannot be edited or removed lt Global Gene properties that can be referred to in all projects lt Project name Gene properties that can be referred to only within a project Category category Cluster properties only lt DomClust Property corresponding to the DomClust results lt Homology Cluster Property corresponding to a homology cluster lt Cluster Property corresponding to a cluster lt Sub Cluster Property corresponding to a sub cluster 119 RECOG Client User s Manual 29 3 Editing properties The property name and type can be modified L To display the Gene _Property Cluster Property screen click Option Gene Property Cluster Property List To display the Edit gene property screen select the property to be edited on the Gene Property Cluster Property screen and click the Edit button Edit gene property Name Expression Type Num Enum elements Multi value On the Edit gene property screen specify the gene property name Name type Type and the presence or absence of multiple attribute values Multi value If the enumeration type is specified specify also the possible values Enum elements in comma delimited form On the Edit gene property screen click the Apply button On the Gene Property Cluster Property screen click the Apply button
96. lts similar to that by single linkage clustering The default value blank is score_cutoff 0 95 or pam_cutoff 0 95 This option specifies whether orthologous or homologous groups shall be created It is simply equivalent to omitting the tree splitting procedure described below by specifying phylocut gt 1 In MBGD orthologous groups are created by splitting the trees of homologous clusters created by the hierarchical clustering algorithm A node with two children A and B is split when Intersect Ph A Ph B min Ph A Ph B gt phylocut where Ph A denotes the set of species contained in node A phylogenetic pattern Ph denotes the cardinality of Ph and Intersect A B is the intersection of sets Aand B This parameter is not effective when ClusteringMode homology is specified When counting the number of species in the above calculation one can incorporate taxonomic information by counting related species only once A taxonomic rank can be specified to determine which set of organisms are considered to be related After the tree splitting procedure described above two clusters 145 RECOG Client User s Manual adjacent clusters of domains are joined when they are almost always adjacent to each other More precisely two clusters A and B are joined when adjacent A B max A B gt raaj1 or jadjacent A B min A B gt ragj where adjacent A B is a set of domains belon
97. n Click the Apply button on the Project List screen Project information editing Click File Open Project Project List to display the Project List screen On the Project List screen select the project and click the Edit button to display the Edit Project screen On the Edit Project screen change the project name and server URL After editing click the Apply button on the Edit Project screen to display the details of the edited information on the Project List screen Click the Apply button on the Project List screen 27 RECOG Client User s Manual 6 6 Project removal 1 Click File Open Project Project List to display the Project List screen 2 On the Project List screen select the project to be removed and click the Delete button A warning message appears Click the OK button Confirm Q Delete project Test Project 3 On the Project List screen click the Apply button Note Upon the removal of the project all the analysis results including the DomClust results of the project are removed Note The files created in a project are saved in the following folder in the user s home directory RECOG project project_ name So unnecessary files can be removed by directly accessing this folder 28 RECOG Client User s Manual 7 Switching the RECOG Server The RECOG servers that conduct DomClust analysis and CoreAligner analysis can be switched When a project
98. n Viewer assigns colors to each gene based on the core structure extracted by the CoreAligner analysis and displays a genome map that connects the corresponding ortholog groups by straight lines Upon zooming in the Viewer automatically switches to the detailed gene view see the figure below Ga Genome Comparison Viewer ene PE MB 25 0 25 Banyloliquefaciens Bandiracts Bantiraciy Ranthiracts Berens B cereus Bee a es es ee m_ lt R cereis 25 50 REAM O00010 ABAM 000020 REAM 000030 RBA B anyloliquefaciens WAM OIR 10 Bandiracts Bantiracty Benthracts E BCE 0 01 Beirens BCE 50 5033 codi B cereus l aki i BCZKL wt BCZHDOC BCZHDOC BCZKOO i EA TA B cereus a Ga g Y BCZKS 180 BCSK5 ISI BCzKS IS EcCZKS5I84 105 RECOG Client User s Manual 27 1 Displaying the Genome Comparison Viewer The Genome Comparison Viewer is displayed after the CoreAligner procedure is finished Therefore the Viewer can be displayed in the same manner as that described in 26 1 Running the CoreAligner program and 26 2 Displaying the CoreAligner analysis results Also the viewer can be displayed by clicking View Genome Comparison Viewer on the Core Genome Alignment screen 27 2 Changing the display area 1 To scroll the view area in the direction of the clicked button click Move Left Move Right in the Toolbox on t
99. n the Neighboring Clusters screen Search range of clusters Specify the range of clusters considered to be neighborhood on the PPM table If the range specified is N N clusters above and below each cluster are considered to be neighborhoods of that cluster Range within which genes are considered to be in each other s neighborhood Specify the distance between two genes on the chromosome considered to be in each other s neighborhood Recalculate when the table is re sorted If the order of clusters is changed due to the sort etc of clusters on the PPM and if this column is checked neighborhood gene clustering is automatically executed under the conditions specified immediately before If unchecked the results of the neighborhood gene clustering are cleared after the order of clusters is changed Netehborine Clusters Search range of clusters Range consider to be neighborhood gene B Recalculate when the table is re sorted 92 RECOG Client User s Manual To execute neighborhood gene clustering click the Run button on the Neighboring Clusters screen Upon the completion of the process of neighborhood gene clustering the group of genes considered to be in each other s neighborhood on the PPM is clustered and displayed in the same color Also Neighboring cluster is displayed in Color on the control panel In this figure only the cells having the same color in the same neighborhood in the t
100. ne respectively Using Any more complicate conditions can be specified such as Existence in more than half of each of bacteria and archaea Species Display on the PPM set All The clusters that are present in all the species in the set are displayed Any The clusters that are present in more less than a certain number percentage of species in the set are displayed None The clusters that are absent in all species in the set are displayed Species color Light red Light blue Grey 1 Displaying the taxonomy filtering conditions The taxonomy filtering conditions are displayed in Filter Taxonomy Filter on the control panel lan Selected Clustering root 6 S Bacteriac6 H Bacillales 6 9 Bacillaceae 6 IN Bacillus cereus 4H187 IN Bacillus cereus 4H820 IN Bacillus cereus ATCC 1096 IN Bacillus cereus ATCC 14579 IN Bacillus cereus B4264 OUT Sp Group Filter A A Taxonomy Filter 29 aa Bacillus cereus 4H187 Bacillus cereus AH820 9 None 1 Oceanobacillus iheyensis HTE831 29 Any Bacillaceae 20 0 2 Bacillus cereus ATCC 10987 Bacillus cereus B4264 62 RECOG Client User s Manual 15 2 Setting the All conditions 1 Select the species on the Taxonomy Tree in the upper part of the Selected tab 2 Click the right mouse button and click Taxonomy All to display the registered species in Filter Taxonomy Filter Al
101. ng the color settings on the Color tab on the control panel i e the same color settings in the PPM table are used 111 RECOG Client User s Manual Color Reference genome Use the color of the control tree 27 14 Automatic correction of the gene orientation In accordance with the setting for the automatic correction of the gene orientation the gene orientation is made uniform in the ortholog group displayed in the center The setting for the automatic correction of the gene orientation is valid only in Adjust Mode View Color Arange Scale Arrangement of orthologous genes Arranged in the positive direction Arranged in the consensus direction of the core genome Arranged in the direction of the reference genome 1 Click View View Change on the Genome Comparison Viewer screen 112 RECOG Client User s Manual Click the Arrange tab on the screen for changing the display of the Genome Comparison Viewer screen 2 Specify the method of automatic correction of the gene orientation on the Arrange tab Arrange in the positive direction Place all genes in the positive direction Arrange in the consensus direction of the core genome Place all genes in the consensus direction of the ortholog group obtained by the CoreAligner analysis Arrange in the direction of the reference genome Place all genes in the direction of the reference genome
102. ntity Alignment coverage Alignment coverage for domain spitting Score cutoif for domain splitting Sknlarty meseure tor orthology score pan Cort DP score IPAM oistence fpercentilertty tring S S lt CSsSY Best ht crterion none Obidrec CQunidirec Cufoft ratio of the score against the best Score tor missing relstionshigs Chastering Mode Cott ratio of paralogs for free seling Overleg ratio radj1 for merging acfacerd clusters Coverage ratio radj2 tor absorbing agacer small clusters Relalive weight for horiz transfer Use deenclust dump After specifying the DomClust analysis result name and parameters click the Run button to display the progress screen and execute the DomClust analysis Click the Run in background button on the progress screen to execute the DomClust analysis in the background In this setting other operations can be performed concurrently To see the progress screen of the DomClust analysis that is underway in the background 37 RECOG Client User s Manual double click the progress bar displayed at the bottom right of the screen Update data Ortholog Clustering DomClust Reading Ortholog Clustering DomClust Sorting Ortholog Clustering DomClust Indexing Ortholog Clustering DomClust Clustering Ortholog Clustering DomClusty Create Result Table Reading Cluster File Run in background Upon
103. obacillus kaustophilus HT4 426 OUT Geobacillus thermodenttrificans NG8O z 33 RECOG Client User s Manual 2 To cancel the selection of the ingroup outgroup species select and click the relevant species or taxonomic group on the Taxonomy Tree and click Group Cancel To cancel all species or groups click Cancel on the uppermost root node 8 4 Automatic ingroup outgroup specification The best way to evenly select the species to be analyzed is to select a representative species for each taxonomic rank RECOG can automatically select a representative species from each taxonomic group for choosing the target species Here the weight of species is determined by the date of publication of the genome sequence that is the earlier the determination of the genome sequence the higher its significance 1 From the Rank drop down menu located above the Taxonomy Tree specify the normative taxonomic rank 2 On the Taxonomy Tree select and click the taxonomic group with a rank higher than the normative rank specified above to be subjected to analysis 3 Click the right mouse button and click Group Auto Ingroup or Auto Outgroup From among the selected classification groups the species with the highest weight is chosen as ingroup outgroup species for each normative rank taxonomic group All Selected Clustering Selected Clustering Rank family v Rank family v A root 598 A root 598
104. off percent identity Alignment coverage Alignment coverage for domain splitting Score cutoff for domain splitting Similarity measure for orthology Best hit criterion Details This value specifies a cutoff E value for the BLAST results The maximum value is 1e 2 Note that in MBGD the E value is adjusted so that the size of the search space the database size times the query length is 1e9 Cutoff score of the optimal local alignment with the JTT PAM250 scoring matrix Jones ef al 1992 The same cutoff is used for both the selection and the clustering steps when score is used as a similarity measure PAM is a unit of evolutionary distance defined as the number of accepted point mutations per 100 residues Dayhoff et al 1978 The PAM distance is estimated based on the PAM substitution matrix which gives the best alignment score The same cutoff is used for both the selection and the clustering steps when PAM is used as a dissimilarity measure Percent identity is defined as the number of identical residue pairs alignment length 100 The alignment length includes the internal gaps Alignment coverage is defined as alignment length length of the shorter sequence 100 Raising this parameter removes matches only in short regions before the clustering procedure MBGD does not conduct this check by default In MBGD a domain splitting procedure is incorporated in the hierarchical clustering algorithm When merg
105. ojects is displayed The currently displayed analysis results are saved DomClust file DomcClust result files are imported Gene property file Gene property files are imported DomClust results are output in tab delimited format and PPM images are output in PDF format Regarding imperfect genomes the contig alignment sequence direction etc on the chromosome are set The size of the PPM image to be saved is specified The local genetic data are updated The RECOG Client is terminated View menu View Tool Run Option gb Ageregate Mode Expand Taxonomy Tree Collapse Taxonomy Tree Select all clusters on PPM PPM Label ia Histogram Taxonomy Tree Pane Information Pane Color genes by properties The PPM display mode is switched between the aggregate mode and the disaggregate mode Regarding the analysis of sort etc whether to conduct an analysis based on clusters or sub clusters is specified The tree in the taxonomy browser is expanded one level The tree in the taxonomy browser is collapsed one level All the clusters on the phylogenetic pattern map PPM are selected 16 RECOG Client User s Manual PPM Label Whether to display the gene name or the cluster ID in the label display fields on both sides of the PPM is specified Color genes by properties Each gene on the PPM is classified by color in proportion to the gene property value Histogr
106. onomy Any New For all any conditions Any condition shown below The Any conditions are changed to the clicked Any conditions Control Sp Group Set H Fitter a O Taxonomy Filter a 9 Alc Bacillus cereus 4H187 Bacillus cereus 4H820 Slee pany Bacillaceae gt 20 0 Bacillus cereus ATCC Rename Bacillus cereus B426 Os Edit E Gene Organism Count Filter Disable For all Any Conditions Keyword Search Delete One or more Gene Set Filter 0 OF more Cluster Set Filter 40 or more H Organism Column 60 or more IN Bacillus cereus 4H187 80 or more IN Bacillus cereus 4H620 20 or less IN Bacillus cereus ATCC 10987 40 or less IN Bacillus cereus ATCC 14579 60M or less IN Bacillus cereus B4264 80 or less nut Oeeannhacilliis ihewensic HTFA31 Setting the None conditions Select the species on the Taxonomy Tree in the upper part of the Selected tab Click the right mouse button and click Taxonomy None to display the registered species names in Filter Taxonomy Filter None on the control panel The relevant species 66 RECOG Client User s Manual names are displayed on the tree in grey 5 root 6 9 Bacteria 6 H Bacillales 6 H Bacillaceae 6 IN Bacillus cereus 4H187 IN Bacillus cereus AH820 IN Bacillus cereus ATCC 10987 IN Bacillus cereus ATCC 14579 IN Bacillus cereus B4264 Taxonomy b All Sp Group b Any
107. ore D C GerefOrgaris Show organism columns 206 o less S _ KeywordSea Color oresnism gt ceB 4B or less SJ Cene SetFite Organism set gt 60 or less D Z Custer Set Fa l kA 80K or less Cenaniem Prime V O phylogenetic pattern 3 s RECOG Client User s Manual Specify the Any conditions on the Any Threshold screen Count Specify the conditions for the number of species in a cluster lt or less The number of species is lower than or equal to lt or more The number of species is higher than or equal to Example 1 The conditions or more 3 or less 5 are met if the number of species in a cluster is 3 or higher and 5 or lower Example 2 The conditions or more 5 or less 3 are met if the number of species in a cluster is 5 or higher or 3 or lower Note the use of and and or in the two examples Percent Specify the conditions for the percentage of species in a cluster lt or less The maximum number of species accounts for of all lt ormore The minimum number of species accounts for of all Example 1 The conditions or more 30 or less 50 are met if a species in a cluster accounts for between 30 50 Example 2 The conditions or more 50 or less 30 are met if a species in a cluster accounts for 50 or more or 30 or less After specifying the Any conditions click the Apply button on the Any Threshold screen to display
108. p is mandatory while the specification of outgroup is optional If the outgroup is specified groups are severed in creating an ortholog group so that the ingroup species form a single phylogenetic group against the outgroup species 1 On the Taxonomy Tree select and click the relevant species or taxonomy nodes 2 Click the right mouse button and click Group Ingroup or Outgroup The selected species are chosen as the ingroup or the outgroup species respectively IN is displayed for the ingroup species and OUT is displayed for the outgroup species H Bacillales 43 N Bacillaceae 22 q Bacillales 43 eens FiB42 Bacillaceae 22 Bacillus anthracis Ames Ancestor 420 IN Bacillus anthracis Ames Bacillus amyloliquetaciens FZB42 IN Bacilus anthracis Sterne Bacillus anthracis Ames Ancestor 420 IN Bacillus cereus ATCC 10987 a Bacillus cereus ATCC 14579 Bacillus cereus E33L Bacillus cereus NYH 391 98 Bacillus thuringiensis serovar konkukiar Ba Color gt Outeroup Bacillus thuringiensis AI Hakam Bacillus cereus E Auto Ineroup Bacillus weihenstephanensis KBAB4 Bacillus cereus Auto Outeroup Bacillus clausii KSM K16 Bacillus thuringie Cincai Bacilus halodurans C 125 Resilhic thi winai Bacillus licheniformis ATCC 14580 DSM Bacillus licheniformis DSM 13 ATCC 14 Bacillus pumilus SAFR 032 Bacillus subtilis 168 Exiguobacterium sibiricum 255 15 OUT Ge
109. p to be subjected to analysis 8 1 Expansion Collapse of the Taxonomy Tree The classification hierarchy of the Taxonomy Tree can be expanded or collapsed in a stepwise manner by clicking the Toolbox buttons For expansion click Expand Taxonomy Tree in the Toolbox One expansion increment is made for each click For collapsing click Collapse Taxonomy Tree in the Toolbox One collapsing increment is made for each click 8 2 Specification of a set of classification ranks to be displayed on the Taxonomy Tree Users can choose a set of taxonomic ranks species genus family order etc to be displayed on the Taxonomy Tree 1 Click W6 Option in the Toolbox to display the Option screen 2 On the Option screen click the Taxonomy Tree tab 3 On the Taxonomy Tree tab s Display Rank form specify the classification rank to be displayed 32 RECOG Client User s Manual All All the taxonomic ranks are displayed Select Only the checked taxonomic ranks are displayed Click the Default button to return to the default settings ace Option 8 3 Specification of the ingroup outgroup On the All tab users can choose a set of species to be compared by the DomClust program Specify a set of species belonging to the interested phylogenetic group as ingroup and specify as the need arises a set of distantly related species for comparison as outgroup the specification of the ingrou
110. pecies azciesiccsn discs hace ccesidcuisdiitessaccecstacsctuidicounednieatedsialesovecdadtonseceetneuidowentaecteie 715 E eo ON eee een ca eee ee ee ee ees 76 19 i Displaying the lst of pen s icone cde cacesce act bencn get vet weceacetatdanctaslectj a 76 19 2 Sorting the list oan ci gt ee re ene oe en ee ee ORE nen Sere renee enter ee 76 19 3 Saving the list of genes wove cece ce ceccecescessecesseueeeeseuseveeseeseusevsesessevsevesseuseseeseeseuseueeseuseuseveseusesesenss 76 20 Display and Operation of the Circular Genome Map CGM ccccscssscsssssesessssesessesesesessesscsesesersesecaeseseees 77 20 L MVS Ry MN AI cs ce ace AAR AERA AREA AA ANETAR 77 20 2 Changing the selected FE CIO ae ecciicasa see ietaace eecala idcaeedcndc itu eeeealts easiness ene ececelesinteoiteeebaes 78 20 3 Linkage between the PPM and CGM ouuw ccc cece cece see ceeeeseeseeceseesousessesseseuseuseseuseusesesseuseeseeenses 78 20 4 Changing the color of NCS cscs cccesasonccdind cacccetecanzdce ctionentedledeausanacessiecoletenanbiacdsasiscusdusladoladnonsicaciuntlecues 78 20 5 Displaying gene information in a DrOWSEL Luu ieee cece cescesee see cescescesessesceesesesseuseseuseesesseveeseuseveeseusannees 719 21 Display and Operation of the Regional Genome Map RGM c cccssscsssssesessesesesesseseseesessesesesereeserseseseees 80 2h Diplavne the RON aeeer ene errr nd nr EE rt Uren gS EP DST Eee PS Un ee Toate ne eT 80 21 2 Zooming in out on the RGM sreiniascavna
111. pecify whether to sort for each cluster aac Cluster Mode or designation is not effective Cluster Mode Sorting is carried out for each cluster If a sub cluster belonging to a cluster contains at least one species sorting is carried out given that the cluster contains at least one species Sub Cluster Mode Sorting is carried out for each sub cluster 2 Click the right mouse button on the PPM select Sort on the pop up menu and click the sort method on the sub menu Sort and display the phylogenetic pattern on the PPM as per the specified sort method However for Gene order and Phylogenetic pattern similarity the species or cluster to be sorted depends on the location on the table of the clicked point 56 RECOG Client User s Manual Sort method Details Category gene name The data are sorted by function category gene name Gene order on lt genome name gt The data are sorted in ascending order of the position of the specified species on the genome Phylogenetic pattern lexical order The data are sorted in lexical order of the phylogenetic patterns Phylogenetic pattern similarity based on the The data are sorted in order of similarity to the cluster phylogenetic pattern of a specified cluster As the similarity indicator specify one of the following 1 Normalized hamming distance 2 Correlation coefficient 3 Correlation coefficient absolute 4 Mutual information Phylogenetic pattern cluster PhyloPatClu
112. r s Manual 30 4 Registering additional genes clusters to a gene cluster set The cluster and the genes contained in a cluster selected on the PPM can be added to a registered gene cluster set 1 Select a cluster on the PPM 2 To add the genes cluster to a registered gene cluster set select a gene cluster set in Gene Set Cluster Set on the set control panel click the right mouse button and click Add selected genes clusters to 30 5 Removing a gene cluster set 1 In Gene Set Cluster Set on the set control panel select a gene cluster set click the right mouse button and click Delete gene cluster set 2 To remove the gene cluster set click the OK button when the warning message is displayed 30 6 Referencing the list of gene cluster sets On the Gene set Cluster set screen the list of registered gene cluster sets can be checked 1 To display the Gene set Cluster set screen click Option Gene Set Cluster Set List 2 To display the gene property click the Gene tab and to display the cluster property click the Cluster tab On each screen the following items are displayed 125 RECOG Client User s Manual Name property name Location location for saving Gene properties only lt Global A gene property that can be referred to in all projects lt Project name A gene property that can be referred to only in the named project Gene Count the gene count of a gene set Gen
113. r setting based on a combined cluster set condition See 31 Combined set Gene count Color setting based on the gene count in a cell See 11 6 Color change according to the gene count in a cell Base color Standard color setting See 11 5 Changing the color of the PPM cell boundary 10 2 4 Phylogenetic pattern registration Phylogenetic Pattern The profile used in the similar phylogenetic pattern search function is displayed For the operation procedure see 33 Similar phylogenic pattern search 10 2 5 Organism column setting Organism Column The species to be displayed on the PPM is displayed For the operational procedure see 18 Changing the display order and display nondisplay of species 10 3 Display of the set management panel Click the Selected tab on the right of the screen and click the Set button below to display the set management panel 44 RECOG Client User s Manual 10 4 Operation of the set management panel On the set management panel the following sets are displayed and can be operated Gene Set Gene Set Combination Cluster Set Cluster Set Combination Organism Set Gene sets are displayed See 30 Registration and management of gene sets cluster sets Combined gene sets are displayed See 31 Combined sets Cluster sets are displayed See 30 Registration and management of gene sets cluster sets Combined cluster sets are display
114. rence are specified and if a cell contains multiple genes specify the method of determining the representative value for graph display lt Min The minimum value among multiple genes is used lt Max The maximum value among multiple genes is used lt Median The median among multiple genes is used lt gt Average The mean value of the properties of multiple genes is used 5 To display the graph on the Histogram tab click the Apply button on the Histogram screen The numerical values displayed on the Value and Difference graph can be switched between display nondisplay on the popup menu Show value displayed upon right clicking on the graph 23 3 Switching between the display nondisplay of the 90 RECOG Client User s Manual Histogram tab 1 To display the Histogram tab on the right of the screen choose and check from the menu View Information Pane 2 To hide the Histogram tab uncheck View Information Pane 91 RECOG Client User s Manual 24 Clustering Neighborhood Genes This function groups genes that are located in the vicinity of each other on the phylogenetic pattern map PPM table and in terms of the genome sequence and assigns a color for each group 24 1 Execution of the clustering of neighborhood genes ae 1 To display the Neighboring Clusters screen click ese Neighboring Clusters in the Toolbox 2 Specify the conditions for neighborhood gene clustering o
115. rical gene property data between two species is displayed by a bar graph Two species and their gene properties for comparison should be specified Info Histogram bat bea bee I ga gtn oih 7500000 omg oho dhbF EGETI BASBOT BAIO94 6451022 2 HAREE If Value and Difference are specified the numerical data are displayed on the graph upon checking Show value 89 RECOG Client User s Manual 3 If Value and Difference are specified specify also the display range and graph style in the View column Range Specify the display range To automatically specify the display range as between the minimum and the maximum values of the target property click the Auto range button Graph Style Select one of the two graph styles Bar bar graph or Line line graph 4 To set the following conditions click the Option button Representative value of multiple property values for a gene If Value and Difference are specified and if multiple values are set for a gene property of a gene specify the method of determining the representative value for graph display lt Min The minimum value among multiple values is used lt Max The maximum value among multiple values is used lt Median The median among multiple values is used lt gt Average The mean value among multiple values is used Representative value of multiple genes in a cell If Value and Diffe
116. roup After specifying the conditions click the Run button The progress screen is displayed and the analysis by the CoreAligner program starts Upon the completion of the analysis the Core Genome Alignment screen and the Genome Comparison Viewer screen are displayed tid Core Genome Alinnment Overview e ee ee ere e e e P cemginos Pcerugnesa P cemgnese Puundocine P entomophila P fluorescens P flucrexens P putida Pputda Puen Pyringae Magnified view Paringar Psyringae 98 RECOG Client User s Manual 26 2 Displaying the CoreAligner analysis results The previously executed CoreAligner analysis results are displayed 260 3 Click Ll Open files in the Toolbox The Open file screen is displayed On the Open file screen select the file filter Core Genome File coaln coregenome and then select the project and CoreAligner analysis result file Upon selecting the CoreAligner analysis result file the information on the analysis results is displayed on the right of the screen Click the Apply button on the Open files screen to display the selected CoreAligner analysis results and DomClust results Components of the core structure display Ortholog group A longitudinal gene group corresponds to an ortholog group Node Each node is represented by a circle or square Shape Details Contains only one gene a Contains two or more genes inparalogs Line
117. s MBGD does not use such a criterion in the selection step by default since the UPGMA algorithm itself must involve it but in some situations it might be useful for the purpose of filtering out some apparent paralogs before clustering See the next section for details This parameter is not effective when the best hit criterion above is not used Orthology need not be a one to one relationship As the bi directional best hit criterion two genes a b are considered to be orthologs when score a b satisfies score a b max max_y score a y max_x score x b 100 gt cutoff_ratio where x and y are any genes of genomes A and B respectively Using cutoff_ratio 100 corresponds to the exact bi directional best hit criterion Similarly as the unidirectional best hit criterion two genes a b are considered to be orthologs when score a b min max_y score a y max_x score x b 100 gt cutoff_ratio Although the usual hierarchical clustering algorithm requires a complete similarity dissimilarity matrix here only significant similarities found by the search are used This option specifies a value to be assigned for the relationships missed by the search The value must be smaller larger than the similarity dissimilarity cutoff Specifying an extremely small large value will result in a classification similar to that by complete linkage clustering whereas specifying a value close to the cutoff gives resu
118. s 138 33 6 Removing the phylogenetic pattern similarity S arch uo ce ceeescsseesescesseccessessesseseessensasseseasens 139 34 Downloading the Sequence information u cceccccececesccesecscessesceeessesseeeesesseveesesseusenseseeseuseveeseusesevesseusensenees 140 34 1 Downloading the Sequence information uu cece cece cee cesceseecescescesescessessesesseuseeseeeeseuseveeseuseveeeenenees 140 35 Management of External Resource URL S c cccssccsscessessecsssseseecescessecsecsessessessessesassecsersessessessesatsatsasseseateeee 142 39 1 Registering an external resource URL wie cece cece ses ceeeesescosseseesousesseseesensessesesseuseeesseuseeeesens 142 35 2 Editing an external resource I ac scien cata cece cee caine ctacee bandana gediasdes Ceaedacedcenteucaay 143 39 3 Removing an external resource URL wie eee ce cesceeee ses ceeeesesseeseseeseuseuseveesessessevesseusevensenseneneees 143 e L112 Oc g amp gt Ge Renna ET EPTE an Et oe en RC eS eRE ET Ur RPO PTR PER SE SIORED NY oS eR EHR RE neESE UTS Per ce oe eet aw nee nega LES A a 144 36 1 DomClust parameters n cceccccccccsccccecsceececessesseeeeseuseeseseuseuseveesessevsesesseuseveeseusessuseesesseuseseuseseevesseuseneeeees 144 Be FM 20 ecasiaavecursastcsiedesiagsreniecasas vacua cvidsdnnresiicad sedans nanan asa dali kag vaste rena ela aeadannnaeaeea eee eeie 147 RECOG Client User s Manual 1 Outline of RECOG 1 1 What is RECOG Ortholog groups Clusters RE
119. s not removed by the above uninstallation procedure If you do not need it remove it manually 3 5 Uninstallation of RECOG for Mac 1 Remove the following directory manually Application recog app Library Receipts recog client pkg 2 The data directory Users lt user account gt RECOG is not removed by the above uninstallation procedure If you do not need it remove it manually 3 6 Uninstallation of RECOG for Linux 1 Remove the recog directory manually 2 The data directory home lt user account gt RECOG is not removed by the above uninstallation procedure If you do not need it remove it manually 12 RECOG Client User s Manual 4 Starting and Terminating RECOG 4 1 Starting RECOG Windows Click Start All programs RECOG RECOG menu Mac Open Applications in the finder window and double click the RECOG icon Linux From the terminal move to the recog directory and execute the following command 4 2 Terminating RECOG On the menu screen click File Exit 13 RECOG Client User s Manual 5 Display and Operation of the RECOG Main Window 5 1 Screen structure EI RICOG vercion 1 1 2 Toot chartes 29000016 out Fie Ver Toot An Ostin JH we G mPORt p vy SRE Hortror a Zoo Traraition state transcriptional reg Gutter GoneMe Cererpton meton state tre 3 Oreste leone Amon porh Douurococos ia fe ayo 2i The main win
120. senin lt o o o oZ oOo O ada Ada regulatory protervs O methyiguanine DNA m a a r LA m loss BCEs264_Ass4adaA Ada reg rvG O methyiguanine DNA m 63740 BCAHIS _AS7iadsA BCAH320_3751adsA 020291315 5 09178102 90379510485 5 029141085 02039 10185 02049 1 6485 02086 1 485 02087108 5 02201108 5 02312 16485 S027 108 2 02822108 ripe pa62 rocR2 teri ani Se ee ptional reguistory protein rrer POA Trancervdinnal rare tadnr ra dab criptional regu stor putative F Display onty matched genes M Highight matched genes 73 RECOG Client User s Manual Check Display only matched clusters on the Keyword Search Result screen to display and only the searched clusters on the PPM Upon unchecking all the clusters are displayed Check Highlight matched clusters to highlight the searched clusters Upon unchecking the highlighting is cancelled Click the color setting column to set the highlight color 17 3 Redisplaying the search results o Click Keyword Search in the Toolbox to display the Keyword Search screen On the Keyword Search screen click the Show search results button to display the last search results 17 4 Enable Disable filter settings by the search results Select Filter Keyword Search on the control panel click the right mouse button and click Enabl
121. snees 99 26 3 Components of the core structure display cc cece cee cesceseesescescessesessesseseesosseaseveeseuseveeseasensnses 99 204 CSA EV SAY OSI Meise cst ca nant iea elt pdeateceeamdea tities 100 20 Selecting an ortholog 0 tacts esa cac sascaasenecteacacuat tens ananin aieiai riirii iniinis 100 26 6 Locating an ortholog group at center uu cceesscescseeesesceseesessesseseeseusesseseeseusesseseuseseveeseuseeeesees 100 26 7 Setting a reference genome gt ene eee een ee EI ener nc St nee a RTE nee EN CE 100 26 8 Display Nondisplay of SOC CIGS pasiccnvacecniveasaviicarniietonssinsicecandnticencnaia vee odeiundsns aietiswuididvihwuledatotneninanehansisearsens 101 26 9 Changing the display order Of species u ee cece ccsceeeecsceeceseesesceseesesseeesesseusesseseeseusesseseusesseeeuseuseeensens 101 26 10 Resetting the window SIZE ou ceccsescescesceseecssessesessessesessesseesessesesseusesesseusesesseaseseeseesausevenseusensneens 102 26 11 Changing the display style of species NAMES ou eee ccs c see ce ces cesceeescesceseesesseveesesseuseveesenseneneens 102 26 12 Changing the ortholog group NA CNS sca cise ccc sect acuwasedaceetanttlaccaehaelenacbiedecamnatlaaeiantieceaaned 102 ASA DIN APAP eeepc EEN EE E EAE E A O ET 103 26 14 Searching by gene name Locus Tagiiwi cceecsssscesssesessecesesesescscecsvesesescevavsveseseesavaveneseseevavaveveneeeetesen 103 26 15 Printing the core structure IAD a cescccicccecia ese ceenceceneiadauceeniiea
122. st Phylogenetic pattern clustering is carried out and the data are sorted according to the hierarchical tree Homology Cluster ID The data are sorted by the homology cluster ID cluster D sub cluster ID Gene properties The data are sorted based on the specified gene properties see 12 3 13 2 PPM sort in the aggregate mode In the aggregate mode the data are sorted based on the phylogenetic pattern of the aggregated Phylogenetic pattern lexical order Select Organism Phylogenetic pattern frequency v Disageregate Mode Phylogenetic pattern similarity based on the cluster Phylogenetic pattern clustering PhyloPatClust _ clusters 1 Click the right mouse button on the PPM click Sort on the menu and click the sort method on the sub menu to sort and display the phylogenetic patterns on the PPM 97 RECOG Client User s Manual Sort method Details Phylogenetic pattern lexical order The data are sorted in lexical order of the phylogenetic patterns Phylogenetic pattern frequency The data are sorted in descending order of the occurrence frequency of the sub clusters with phylogenetic patterns Phylogenetic pattern similarity based on the The data are sorted in order of similarity to the cluster phylogenetic pattern of a specified cluster As the similarity indicator specify one of the following 1 Normalized hamming distance 2 Correlation coefficient 3 Correlation coefficient absolute 4 Mut
123. syrthests 41 4 Arosat amiro acid teenity 1 2 Aspartate fasity 1 3 Branched chain fanty 14 Caternate family 15 Pyruvate landy 1 6 Siira liniy 1 7 Hstidna farnty 2 Punines pyrimidines racicomdes and muciootiges 2 4 Z Deoxyriboraclontide metabolism 2 2 Nxlecide and rexiooude rterconversions 2 3 Purine rorscioctide biosynthesis 2 4 Pyresdine rhorwciecntide bosyrthesis 25 Salvaje of nucieosices and nuciedtides 25 Suagae tescloctice bins yntherstit tend Goerwer tines O Use the color of the control tree Lasse restore creste core _ 21 5 Displaying gene information in a web browser lif By double clicking a gene you can display in a web browser the informationof the default external resource that is set according to 35 External Resource URL Management You can also click the right mouse button on a gene and choose an external resource URL to display 82 RECOG Client User s Manual 22 Multiple Alignment and Phylogenetic Tree Multiple alignment among genes belonging to a cluster can be created using the ClustalW program Also a phylogenetic tree can be created and displayed based on the results of the multiple alignment 22 1 Execution of multiple alignment Note Multiple alignment can be executed only in an environment where Internet connection is available 1 Specify the execution parameters of ClustalW Clicking Ve Option in the Toolbox to display the Option screen
124. ter 3 On the Download sequence screen select amino acid sequence or DNA sequence Protein Download the amino acid sequence DNA Download the DNA sequence For the DNA sequence the extra sequence count obtained upstream and downstream and the delimiting letter between the extra sequence obtained and the gene DNA sequence can be specified 4 In Target genes specify the target gene All genes on the cluster table The genes contained in all the clusters displayed on the PPM are the targets Genes included in the selected cluster The genes contained in the cluster currently selected on the PPM are the targets 140 RECOG Client User s Manual 5 After specifying the conditions click the Apply button When the screen for file saving is displayed enter the file name and click the OK button 141 RECOG Client User s Manual 35 Management of External Resource URL s To display the information on external resources in a web browser from the Info tab and the Regional Genome Map register the external resource URL s 35 1 Registering an external resource URL 1 Click Option URL to display the URL screen http Jimbgd genome ad jp Organism LocusTag 2 To display the Edit URL screen click the Add button on the URL screen FRECOG RECOG_gene_info_frame pl spec 1 amp name 2 Organism LocusTag 3 On the Edit URL screen specify the name of
125. ter editing the profile click the Apply button 33 3 Removing a profile 1 Select a profile in Phylogenetic Pattern on the control panel click the right mouse button and click Delete pattern When the warning message is displayed click the OK button 135 RECOG Client User s Manual 33 4 Similar phylogenetic pattern search 1 To display the Calculate distance by pattern screen select a profile in Phylogenetic Pattern on the control panel click the right mouse button and click Calculate distance by pattern Calculate distance by pattern Calculate distance by pattern Name Name Profile Profile Phylogenetic pattern Phylogenetic pattern Gene property Start Type of distance Normalized hamming distance O Gene property Start Sort by the caluculated result Type of distance Normalized hamming distance Treatment of missing value Ignore Average Specified value Presentative value of multiple gene s property value Min Max Median Average Presentative value of multiple gene in one cell Min Max Median Average Sort by the caluculated result 2 On the Calculate distance by pattern screen specify the conditions for determining the pattern similarity Name column Save column To save the calculation results to a file check the Save column and enter the name If the calculation
126. ters of the same phylogenetic pattern are displayed in the same row in an aggregated manner and no cluster headers are displayed 20 RECOG Client User s Manual ingroup outgroup Homology cluster Subcluster Cluster Outer ortholog group Homology Cluster Inner ortholog group Subcluster 1 Subcluster 2 Outgroup cluster Subcluster 3 Subcluster 1 cluster 2824 1 Nested table structure RECOG screen display 5 8 Info tab The Info tab displays the cluster selected on the PPM and the gene information in that cluster In the aggregate mode multiple clusters with the same phylogenetic pattern are displayed Info Histogram Aminoglycoside N3 acetyltransferase Cluster ID Gene Name Description Aminoglycoside N3 a Organism Locus Tag ber BCAH187_A2976 BCAH820_2929 BCE_2969 BC2919 BCB4264_42939 Contents i bce LocusTag BC2919 GeneName a o OOo e An ler Expression 567 0 1 Cluster description field at the top The cluster selected on the PPM is described 21 RECOG Client User s Manual Cluster information table upper table The cluster information selected on the PPM is displayed When the table is double clicked a browser is activated and the details of the cluster information are shown Also by right clicking the selected cluster on the table various functions including Multiple Alignment and the display of a Regional Genome Map for the selected gene
127. the logical conditions between the sets To add gene cluster sets to the combined conditions select the sets in the Set column and click the gt gt button To add multiple gene cluster sets to the combined conditions as a common set select the sets in the Set column and click the amp gt gt button To add gene cluster sets to the combined conditions as a negative condition select the 127 RECOG Client User s Manual sets in the Set column and click the Not gt gt button To add multiple gene cluster sets to the combined conditions as a common set of negative conditions select the sets in the Set column and click the Not amp gt gt button To remove a condition from the combined conditions select the condition in the Condition column and click the Delete button To modify the order of priority of the combined conditions select a condition in the Condition column and click the Up Down button To change a condition in the combined conditions into a negative condition select the condition in the Condition column and click the Flip Not button To modify the negative condition in each set contained in the combined conditions double click the condition name in the Condition column and modify it on the Edit condition screen displayed El Edit condition Test gene set 1 Test gene set 2 Test gene set 3 Flip Not Delete To modify the color applied to the combined condit
128. this is checked the gene properties retrievable on the RECOG server are searched on that server If unchecked all the gene properties are searched locally Representative value of multiple values set for a gene property If Value and Difference are specified and if multiple values are set for a gene property of a gene the method of applying the search conditions is specified lt At Least One If at least one of the multiple values meets the condition it is considered that the search condition is met lt All If all the multiple values meet the condition it is considered that the search condition is met lt Average If the mean value of the multiple values meets the condition it is considered that the search condition is met This applies only to numerical type gene properties 4 Upon the completion of the search process the Keyword Search Result screen is displayed In Filter Color on the control panel the conditions corresponding to the search result are displayed On the PPM only the clusters containing the searched genes are highlighted Control Sp Group Fitter Taxonomy Filter Gene Organism Count Filter 4 Keyword Search Keyword Search Gene Descritpion r Gene Set Filter Cluster Set Filter Organism Column Sort Color Keyword search Gene Descritpion reguli Set al Keyword Search Result 9 9 9 9 9 o o o o o o o o o o ook E 02356155 _GeneName Organism De
129. ual information Phylogenetic pattern cluster PhyloPatClust Phylogenetic pattern clustering is carried out and the data are sorted according to the hierarchical tree 13 3 Sort based on properties The phylogenetic patterns are sorted based on the gene properties provided by the RECOG server or the gene properties registered as described in 29 1 Registration of gene properties 1 Click the right mouse button on the PPM and click Sort Gene properties to display the Sort by gene properties screen Sort by gene properties B anthracis Sterne Asc AA length Asc v Asc Y v 2 On the Sort by gene properties screen specify the gene properties for the sorting and the ascending order Asc descending order Desc To add the sorting conditions click the Add Condition button 08 RECOG Client User s Manual Click the Option button and the following setting column is displayed Representative value of multiple values set for a gene property If multiple values are set for a gene property of a gene specify the method of determining the representative value for the sorting lt Min The minimum value among multiple values is used lt Max The maximum value among multiple values is used lt Median The median among multiple values is used lt gt Average The mean value among multiple values is used Representative value of multiple genes in a ce
130. us ATCC 14579 IN Bactht cereus 64254 Controt Sp Group Be ACen Set D Gene Set Conbirstion S OY Gere Corbiration 1 Test cere st 1 amp Teal gers sel 2 amp Test gene set3 Tesi cere se 1 3 Test gers sel 2 Tesi cere s 23 Test gare sel S Tesi cere sti amp Test gere sel S Tesi cere 2241 Tesi cere se 2 Tesi cere se 3 E Custer Set I Cluster Set Corkunation S Dy ster Conkination 1 Tesi cluster set 1 amp Test cluster set 2 amp Test cluster set 3 Test cluster set 1 amp Test chester set 2 Test cluster set 2 amp Test cluster set 3 Test cluster set 1 amp Test cluster set 3 Test cluster set 1 SCC SCAHIG A2S22 ECAH 20 2776 BLE 2801 Test chuster set 2 Test chister set 3 ACP SCAHIS7_ASSSO BCAHI20_ 5505 ECE 5539 Bre 2804 BLE 2603 129 RECOG Client User s Manual Silas 31 3 Editing a combined set To display the Gene Cluster set combination screen select a combined set in Gene Set Combination Cluster Set Combination on the set control panel click the right mouse button and click Edit gene cluster set combination Modify the conditions on the Gene Cluster set combination screen For the method of setting the conditions refer to 31 1 Registering a combined set After modifying the conditions click the Apply button Removing a combined set To remove a combined set select the combined set in Gene Set Combination Cluster Set Combination
131. ut on the RGM JE Zoom out in the Toolbox respectively on the Regional Genome Map screen Display Nondisplay of the Locus Tag Click LE Label ON OFF in the Toolbox on the Regional Genome Map screen When the button is displayed in color the Locus Tag is displayed and when the button is displayed in grey the Locus Tag is hidden Setting the gene color To display the Color Setting screen click is Color Setting in the Toolbox on the l Regional Genome Map screen 2 Set the gene color on the Color Setting screen Sort Display on the PPM Function Category The color allocated to the current Function Category is used Cluster ID A unique color is allocated to each cluster The color is allocated according to the gradation based on the cluster ID Although it is difficult to distinguish between the colors the allocation remains the same even if the dsplayed region changes Pattern A unique color and pattern are allocated to each cluster The color and pattern are allocated to each currently displayed cluster in the order of cluster size Although the color and pattern are easily distinguishable the allocation changes with the displayed region Use the color The color currently in use on the PPM the color set in Color on currently assigned on the control panel is used the PPM 3 Click the Apply button 81 RECOG Client User s Manual Color Setting Function Category 1 Amino ochd Dlo
132. ut on the core structure image click Zoom in Zoom out in the Toolbox on the Core Genome Alignment screen 26 14 Searching by gene name Locus Tag 1 In the column for item selection in the Toolbox on the Core Genome Alignment screen select Gene Name Locus Tag or Both If Both is selected a search according to both the gene name and the locus tag is conducted 2 Enter a keyword in the keyword entry column 3 Click the Search button and the ortholog group to which the searched gene belongs is highlighted on the Overview and the viewing area of the magnified view is scrolled so that one of the ortholog groups hit by the search is displayed in the center of the screen 4 If the Search button is clicked under the same conditions the viewing area of the magnified view is scrolled so that the next ortholog group containing the searched gene is displayed in the center of the screen id Core Genome Alignment e w Fe Fe Fo G 6 S F E vb YD s se FF ha ah Keer ah eh SP a SMP we Ee EE ah eh oh FF a ae ed a ee IISI a a ee ee et ot a Pcenginesa P cemginesa P cereginesa P nendocina P ertomophtla P flucrexens P flucremens Pputda P putida P stutzen Pay rningae Py ringae Payringae 103 RECOG Client User s Manual 26 15 Printing the core structure image 1 Click File Preview on the Core Genome Alignment screen The Core Genome Alignment Preview screen is displayed 2 Click
133. utgroup 3 Click Y Ortholog Clustering DomClust in the Toolbox to display the Execute domclust screen 4 On the Execute domclust screen enter the analysis name in the Name field The result is automatically saved under the analysis name entered here If the default parameter set is used select Default parameters if the parameter set executed immediately theretofore is used select lt lt Last Parameters gt gt if DomClust is conducted using a parameter set saved previously select the parameter set saved in the Parameter set field ta Execute domclust Q Start Ortholog Clustering DornCusty Name cluster _2008xxXXx ingroup 5 Outgroup 1 frente eau Prone JE RECOG Client User s Manual To specify a new parameter set click the Parameters button and set it on the displayed parameter setting screen For details on the parameters refer to 37 1 DomClust Parameters To save the parameters that were set on the parameter setting screen click the Save parameters button To remove the saved setting specify the parameters to be removed in the Parameter set field and click the Delete this parameter set button bel Execute domclust Start Oriholog Clustering DorChsty Name cluster_2009XXXX Outgroup 1 Farts ersa Parana z Orholog Clustering Domt kest Setting Delete this paramler set Cott BLAST E value Cutoft DP score Cufott PAM distance Cutott percert ide
134. value If this is checked the threshold value is automatically divided equally in consideration of the possible range of the properties immediately after the change thereof 03 RECOG Client User s Manual lt Color of genes don t have the gene property This is used to set the color of the gene with no specified property value be Color genes by properties Organism ll Property lAa length Remove color Ario value Value Rank The method for assigning arank Al species O Every species actomelically update value Coker of genes dont have the gene property LJ If the properties are of the enumeration type lt Set the color for each possible value lt Color of genes don t have the gene property This is used to set the color of the gene with no specified property value Ed Color genes by properties Organism All Property estat a A Coke of genes dont have the gene property al RECOG Client User s Manual 3 Click the Apply button on the Color genes by properties screen Each cell is displayed in color as per the conditions specified on the PPM BAIFA 5d GX0030 GTNG_0029 TENES abrB ENTERT EPSEN GTNG_2665 AFERE acci BCE 3533 acca BAsd039 BCE 4258 2400 CTNC 2331 accB BASdO38 M2398 GTNG_2330 081385 acct BAS4495 2742 GTNG_2866 need HI HIRERT 083010 EGG BASIO52 GTNG_0533 0E2404 ace BASIOBS BCE_1228 062405 aceB BAS4535 60463 KEREN GTNG_268
135. word search See 17 Keyword search Gene Set Filter Filtering by combined gene set condition See 31 4 A combined set is set as the filtering condition Cluster Set Filter Filtering by combined cluster set condition See 31 4 A combined set is set as the filtering condition 10 2 2 Sort setting Sort The sort condition that is applied to the PPM is displayed in the Sort folder of the control panel For the operational procedure see 13 PPM sort 10 2 3 Color setting Color In the Color folder on the control panel the gene cluster color that is displayed on the PPM and the comparative genome map view is set The coloring is applied in descending order of the alignment sequence on the control panel and is overwritten the upper one has priority over the lower one The order can be changed by dragging and dropping an object Also the color settings can be enabled disabled by clicking Enable Disable The following color settings can be specified 43 RECOG Client User s Manual Gene property Color setting based on gene cluster property See 12 Coloring by property Neighboring cluster Color setting based on the result of neighboring gene clustering See 24 Neighboring gene clustering Keyword search Color setting based on the keyword search result See 17 Keyword search Gene Set Color setting based on a combined gene set condition See 31 Combined set Cluster Set Colo
136. yword Search Cluster Gene All species AND v AND v vi Add Condition Clear Condition Show search results Close For the search the following marks can be entered in the keyword entry column Type of search Example Match search Word Partial match search word Prefix search word Suffix search word Or more gt 10 Or less lt 10 More than gt 10 Less than lt 10 With keyword inside ABC Without keyword inside word Multiple word search word word2 Phrase search wordl word2 Genes that include a phrase matching word are searched 6 Genes that include the phrase lt word are searched Genes that include the phrase word are searched Genes that include the phrase word are searched Ten or more genes are searched Ten or less genes are searched More than ten genes are searched Less than ten genes are searched Genes with word inside are searched Genes without word inside are searched Genes that include word1 or word2 are searched Genes that include word and word2 as a phrase are searched In the Description field a partial match search is conducted 72 RECOG Client User s Manual The inequality sign is valid only for numerical type gene properties 3 Click the Option button to specify the following conditions Search on the server If
137. yzed The taxonomic tree of all the species registered in the RECOG server is displayed On the tree screen it is possible to choose the species ingroup outgroup for DomClust analysis and to color the species 2 Selected tab for PPM manipulation This tab consists of upper and lower views The upper view displays the taxonomic tree for the organisms shown on the PPM that are currently targeted for analysis On the tree screen phylogenetic pattern filtering conditions species groups efc can be set The lower view changes by selecting one of the following upper buttons Control A view for controlling the display of ortholog table including the color settings filter settings sort settings and the switching of the order of display or the display nondisplay of the PPM species is displayed 19 RECOG Client User s Manual Sp Group Species groups are displayed Set Currently registered gene sets cluster sets compound conditions and species sets are displayed 3 Clustering tab The hierarchical clustering tree obtained from phylogenetic pattern clustering is displayed 5 7 Phylogenetic Pattern Map PPM The Phylogenetic Pattern Map PPM is the main feature of the RECOG system In the PPM genes that belong to each ortholog group are listed in a table in which ortholog groups and species are arranged in the rows and columns respectively When the display area is reduced a pattern representing the

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