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Geneious User Manual

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1. Figure 3 6 Options for protein pairwise alignment 3 6 Multiple sequence alignments A multiple sequence alignment is a comparison of multiple related DNA or amino acid se quences A multiple sequence alignment can be used for many purposes including inferring 3 6 MULTIPLE SEQUENCE ALIGNMENTS 61 the presence of ancestral relationships between the sequences It should be noted that protein sequences that are structurally very similar can be evolutionarily distant This is referred to as distant homology While handling protein sequences it is important to be able to tell what a multiple sequence alignment means both structurally and evolutionarily It is not always possible to clearly identify structurally or evolutionarily homologous positions and create a single correct multiple sequence alignment 3 Multiple sequence alignments can be done by hand but this requires expert knowledge of molecular sequence evolution and experience in the field Hence the need for automatic mul tiple sequence alignments based on objective criteria One way to score such an alignment would be to use a probabilistic model of sequence evolution and select the alignment that is most probable given the model of evolution While this is an attractive option there are no efficient algorithms for doing this currently available However a number of useful heuristic algorithms for multiple sequence alignment do exist 3 6 1 Progressive pairwise alignment
2. Download button inside the document view or just above it There are also Download items in the File menu and in the popup menu when document summary is right clicked The size of these files is not displayed in the Documents Table Be aware that whole genomes can be very large and can take a long time to download You can cancel the download of document summaries by selecting Cancel Downloads from any of the locations mentioned above Advanced Search also provides you with a number of options for restricting the search on a field depending on the field you are searching against For example if you are using numbers to search for Sequence length or No of nodes you can further restrict your search with the second drop down box e is greater than gt e is less than lt e is greater than or equal to gt e is less than or equal to lt Likewise if you are searching on the Creation Date search field you have the following op tions e is before or on e is after or on e is between When searching your local folders you have the option of searching by Document type The second drop down list provides the options is and is not The third drop down lists the various types of documents that can be stored in Geneious such as 3D Structure Nucleotide sequence and PDF see Figure 2 3 And Or searches The advanced options let
3. Mark calls Draw a vertical line showing the exact location of the call made by the base calling software Layout Options controlling layout and view Those include X and Y axis scaling size of largest base letter when Sequence logo is on and minimum size of base letter to prevent bases of low quality becoming unreadable 2 7 6 The PDF document viewer This viewer is under development Currently to view a pdf document either double click on the document in the Documents Table or click on the View Document button This opens the document in an external PDF viewer such as Adobe Acrobat Reader or Preview Mac OS X On Linux you can set an environmental variable named PDFViewer to the name of your external PDF viewer The default viewers on Linux are kpdf and evince 2 7 7 The Journal Article Viewer This viewer provides two tabs Text View and BibTex Text view displays the journal article details including the abstract The text contains a link to the original article through Google Scholar below the title and authors Figure 2 17 BibTex is the standard TEX bibliog raphy reference and publication management data format ATEX is a common program used to create formatted documents including this one The information in the BibTex screen can be exported for use in TEX documents 2 8 Preferences There are two sets of preferences General and Plugins You can access the preferences screen in two ways 1
4. The result of a BLAST query is a table of hits Each hit refers to a GenBank accession number and the gene or protein name of the sequence Each hit also has a Bit score which provides information about how similar the hit is to the query sequence The bigger the bit score the better the match 2 2 ACQUIRING DATA FROM PUBLIC DATABASES 21 Finally there is also an E value or Expect value which represents the number of hits with at least this score that you would expect purely by chance given the size of the database and query sequence The lower the E value the more likely that the hit is real Geneious is able to run NCBI BLAST on seven different databases Some of these databases are non redundant in order to reduce duplicate hits You can submit either a raw sequence or Genbank accession number into NCBI BLAST and receive a summary of results for each hit This summary contains the bit score e value identity and the stretch of the query sequence and hit sequence that match The databases that can be searched are Table 2 3 Nucleotide sequence searches in the BLAST databases Database Nucleotide searches env_nt This contains DNA sequences from the environment i e all organisms put together month All new updated GenBank EMBL DDBJ PDB sequences released in the last 30 days nr All non redundant GenBank EMBL DDBJ PDB sequences no EST STS GSS or HTGS sequences pat Nucleotide sequences derived from t
5. alexa drummond Ozaoiegy oxford ac uk IMGACTGACTG ACTCAGATCG ATCGATCGCG CGATATCATC GACTGCGCGT ra Line Weight carp 20372 gt Show Tip Labels par em partial sequences PMID 12136032 Selected 258 residues from residue 21 to 278 a Nucleotide sequence b Journal Article c Phylogenetic tree Figure 1 3 Three document viewers 1 2 4 The Help Panel The Help Panel includes a tutorial If you are new to Geneious we recommend working through the tutorial first Most help is automatic A short help message pops up when any of the tasks on the Services panel are clicked This panel can be closed at any time by clicking 1 2 USING GENEIOUS FOR THE FIRST TIME 9 the X symbol in the top right hand corner If you want to display the help panel click on Help in the Menu Bar and select the small box beside Help The Help Panel will reappear Figure 1 4 O Help Previous 7of21 Next Sequence alignment Geneious allows you to align a set of sequences If the sequences you just imported are not selected select them all now Click on the Alignment button in the toolbar Click OK to accept the default alignment settings When the alignment has finished a new alignment document will be added to the current folder and selected This will display the alignment in the sequence viewer If you are using Geneious pro there is also
6. folder within Geneious If no folder is selected Geneious open a dialog which lets you specify a folder Data from an NCBI EMBL Contacts search Data downloaded from public databases within Geneious will appear in the Document Table and can be dragged from there into a local folder of your choice Important if you don t drag the documents from a database search into your local folders the results will be lost when Geneious is closed 2 1 4 Data output formats Each data type has several export options Any set of documents may be exported in Geneious native format Data type Export format options DNA sequence FASTA Geneious Amino acid sequence FASTA Geneious Protein 3D structure PDB FASTA Geneious Multiple sequence alignment FASTA NEXUS 12 Geneious Phylogenetic tree Phylip phy FASTA NEXUS 12 MEGA3 11 Geneious PDF document PDF Geneious 2 2 Acquiring data from public databases Geneious is able to communicate with a number of public databases hosted by the National Centre for Biotechnology Information NCBI and the European Molecular Biology Laboratory EMBL You can access these databases through the web at http www ncbi nlm nih gov and http www ebi ac uk embl respectively Both are well known and widely used storehouses of molecular biology data 2 2 1 NCBI Entrez and EMBL databases NCBI was established in 1988 as a public resource for information on molecular biology Geneious allo
7. only for a quick and dirty analysis when a rooted tree is needed and the rate of evolution is does not vary much across the branches of the tree 3 8 4 Distance models or molecular evolution models for DNA sequences The evolutionary distance between two DNA sequences can be determined under the assump tion of a particular model of nucleotide substitution The parameters of the substitution model define a rate matrix that can be used to calculate the probability of evolving from one base to another in a given period of time This section briefly discusses some of the substitution models available in Geneious Most models are variations of two sets of parameters the equilibrium frequencies and relative substitution rates Equilibrium frequencies refer to the background probability of each of the four bases A C G T in the DNA sequences This is represented as a vector of four probabilities 74 nc TG mr that sum to 1 3 8 BUILDING PHYLOGENETIC TREES 65 Relative substitution rates define the rate at which each of the transitions A gt G C T and transversions A gt C A e T C e G G gt T occur in an evolving sequence It is represented as a 4x4 matrix with rates for substitutions from every base to every other base Jukes Cantor This is the simplest substitution model 10 It assumes that all bases have the same equilibrium base frequency i e each nucleotide base occurs with a frequency of 25 in DNA sequences and each
8. select the Includes Java 1 5 option This involves downloading a larger file If you are a Mac user and have OS X 10 4 or later you will have to download Java 1 5 from http www apple com support downloads java2se50release3 html 1 3 2 I get a connection error when trying to search using NCBI or EMBL If the message reads Check your connection settings there is a problem with your Internet connection Make sure you are still connected to the Internet Both Dial up and Broadband can disconnect If you are connected then the error message indicates you are behind a proxy server and Geneious has been unable to detect you proxy settings automatically You can fix this problem 1 Check the browser you are using These instructions are for Explorer Safari and Firefox 2 Open up your default browser 3 Use the steps in Figure 1 6 for each browser to find the connection settings 4 Now go into Geneious and select Preferences There are two ways to do this e Shortcut keys Ctrl Shift P Windows Linux Command Shift P Mac OS X e Tools Menu Preferences 5 This opens the Preferences Click on the General tab There are four options in the drop down options under Connection settings Figure 1 7 e Use direct connection Use this setting when no proxy settings are required e Use browser connection settings This allows Geneious to automatically import the proxy settings e Use proxy server This ena
9. uk Significant Digits 43 SS Se SESE 1 Figure 2 15 A view of a phylogenetic tree in Geneious General General has 3 buttons showing the different possible tree views rooted circular and un rooted The Zoom slider controls the zoom level of the tree while the Expansion slider expands the tree vertically Layout This has two options root length and curvature Both Root Length and Curvature can be increased by dragging the bar towards the right Root length is not available for unrooted trees Checking the Align taxon labels box will align the taxa labels to provide easier viewer for large trees Formatting There are a range of formatting options Transform branches allows the branches to be equal like a cladogram or proportional Leaving it unselected leaves the tree in its original form Ordering orders branches in increasing or decreasing order of length but within each clade or 2 7 DOCUMENT VIEWERS IN GENEIOUS 47 cluster Show root branch displays the position of the root of the tree Line weight can be increased or decreased to change the thickness of the lines representing the branches If you are unfamiliar with tree structures please refer to Figure 2 16 for the following options Root Branch Node Tip Figure 2 16 Phylogenetic tree terms Show tip labels This refers to labels on the tips of the branches of the tree Show node labels This refers to
10. 1 Cys peroxiredoxin protein Bosa EA E Fe IE source m gt a v i Colors EX gt A Zoom Options Cys peroxiredoxin protein COS Statistics 147 1596 Cys peroxiredoxin protein mR gt Cys peroxiredoxin protein MRNA length 147 E Frequencies A 40 27 2 C 35 23 8 ETA G 38 25 9 T 34 23 1 GC 73 49 7 Selected 147 residues from residue 525 to 671 Figure 2 10 A view of an annotated nucleotide sequence in Geneious 38 CHAPTER 2 DATA HANDLING Zoom level The plus and minus buttons increase and decrease the magnification of the sequence by 50 or by 30 if the magnification is already above 50 P zooms to 100 The 100 zoom level allows for comfortable reading of the sequence na 4 zooms out so as to fit the entire sequence in the available viewing area Colors The colors option controls the coloring of the sequence nucleotides or amino acids Uncheck the color checkbox to turn off all coloring without viewing further options Coloring schemes differ depending on the type of sequence For example the Polarity and Hydrophobicity coloring schemes are available only for Protein sequences Layout Layout has various options controlling the layout of the sequence e Show tree This toggles the display of the phylogenetic tree when viewing the alignment of a phylogeny document e Show residue positions This toggles the display
11. A global alignment is a sequence alignment over the entire length of two or more nucleic acid or protein sequences In a global alignment the sequences are assumed to be homologous along their entire length 15 3 5 PAIRWISE SEQUENCE ALIGNMENTS 59 3 5 1 Scoring systems in pairwise alignments In order to align a pair of sequences a scoring system is required to score matches and mis matches The scoring system can be as simple as 1 for a match and 1 for a mismatch between the pair of sequences at any given site of comparison However substitutions inser tions and deletions occur at different rates over evolutionary time This variation in rates is the result of a large number of factors including the mutation process genetic drift and natural selection For protein sequences the relative rates of different substitutions can be empirically determined by comparing a large number of related sequences These empirical measurements can then form the basis of a scoring system for aligning subsequent sequences Many scoring systems have been developed in this way These matrices incorporate the evolutionary prefer ences for certain substitutions over other kinds of substitutions in the form of log odd scores Popular matrices used for protein alignments are BLOSUM 9 and PAM 2 matrices Note The BLOSUM matrix is a substitution matrix The number of a BLOSUM matrix indicates the threshold similarity between the sequences origin
12. Mol Biol Evol 4 1987 no 4 406 25 63 64 66 19 TF Smith and MS Waterman Identification of common molecular subsequences Journal of Molecular Biology 147 1981 195 197 58 59 20 DL Swofford Paup Phylogenetic analysis using parsimony and other methods version 4 0 Sinauer Assoc Sunderland Mass 1999 63 21 K Tamura and M Nei Estimation of the number of nucleotide substitutions in the control region of mitochondrial dna in humans and chimpanzees Mol Biol Evol 10 1993 no 3 512 526 65 22 JD Thompson TJ Gibson F Plewniak F Jeanmougin and DG Higgins The clustal x windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 1997 no 24 4876 4882 14 15 16 61 62 23 JD Thompson DG Higgins and TJ Gibson Clustal w improving the sensitivity of progres sive multiple sequence alignment through sequence weighting position specific gap penalties and weight matrix choice Nucleic Acids Res 22 1994 no 22 4673 4680 14 16 62
13. Run The agent will then be added to the list in the agent dialog and it will perform its first search if you clicked Create and Run Otherwise it will wait until its next scheduled search 00 Create Agent Search Database PubMed H Match all 5 of the following contains EE Drummond Deliver To Local 32 He New Folder Search every 1 Days HJ _ Only get documents created after today Cancel 4 Create Create and Run Figure 2 5 The Create Agent Dialog 2 4 2 Checking agents Once you have created one or more agents Geneious allows you to quickly view their status in the agents window which is accessible from the toolbar Your agents details are presented in several columns Enable Action Status and Deliver To Enable This column contains a check box showing whether the agent is enabled Action This summarizes the user defined search criteria It contains 1 Details of the database accessed For example Nucleotide and Genome under NCBI 2 The search type the Agent performed i e keyword 3 The words the user entered in the search field for the Agent to match against 28 CHAPTER 2 DATA HANDLING Status This indicates what the Agent is currently doing The status will be one of the following e Next search in x time eg 18 hours The agent is waiting until its next scheduled search and it will search when this time is reached e Searching These
14. Shortcut keys Ctrl Shift P Windows Linux Command Shift P Mac OS X 2 Select the Tools Menu and click Preferences 2 8 PREFERENCES 49 A virus reveals population structure and recent demographic history of its carnivore host Roman Biek Alexei J Drummond amp Mary Poss Wildlife Biology Program University of Montana Missoula MT 59812 USA rbiek emory edu Science 2006 311 538 41 Google Scholar Directly transmitted parasites often provide substantial information about the temporal and spatial characteristics of host to host contact Here we demonstrate that a fast evolving virus feline immunodeficiency virus FIV can reveal details of the contemporary population structure and recent demographic history of its natural wildlife host Puma concolor that were not apparent from host genetic data and would be impossible to obtain by other means We suggest that rapidly evolving pathogens may provide a complementary tool for studying population dynamics of their hosts in shallow time PMID 16439664 Figure 2 17 Viewing bibliographic information in Geneious 2 8 1 General This contains connection settings data storage details for your Local documents Automatic new version checking and Search History Check for new version of Geneious Enable this to have Geneious check for the release of new versions everytime it is started If a new version has been released Geneious will tell you and give you a link to dow
15. WY Annotation Save ja 0 3U 60 gt Z F l A1 KE 00 K GTAGGATGGC CTGAGGTTAG GGAAAGAATG a A1 TZ 97 GTGGGATGGC CTGAGATTAG GGAAAGAATG v M Graphs A SN 96 D GCGGGATGGC CTAAGGTTAG GGATAGGATG similarity A1 UG 99 GTGGGATGGC CTAGGGTTAG GGAAAGAATA SS Ci O A1 KE 00 K AAGGGATGGC CTGAAGTTAG GGAGAGAATG el Similarity S Pa O A gt Consensus A1 KE 00 K AGACGTGCTC GTGCTCCTGC AGCAGCACCT Annotations A1 12 97 AGACGAACTC gt A Layout A SN 96 D AGACAAACTC CTCCA gt M Colors A1 UG 99 AGACAAACTC cT gt E Zoom Options A1 KE 00 K AGAAATACCC gt Statistics 636 85 Similarity Zi TT Oe A1 KE 00 K ACTGCCGCAG CACCTGGAGT AGGAGCAGTT A1 TZ 97 CTACAGCAG CAACAGGAAC AGGAGCAGTA A SN 96 D ACACCAGCAG CAAAAGGAGT AGGAGCAGTA A1 UG 99 CCAGCAG CAGAAGGAGT AGGAGCAGCA A1 KE 00 K CTGCACCAG CACCAGGAGT AGGAGCAGTA Similarity 2 MA MA MA gt Alt left click on a sequence position or annotation or select a region to zoom in Alt right click to zoom out Figure 2 11 The similarity graph for an alignment of nucleotide sequences Hydrophobicity This is available with protein sequences It displays the Hydrophobicity of the residue at every position or the average Hydrophobicity when there are multiple sequences pl pI stands for Isoelectric point and refers to the pH at which a molecule carries no net elec trical charge The pl plot displa
16. a contact Similarly you will occasionally see a dialog box pop up asking you Allow username talk geneious com as contact This is another Geneious user attempting to add you as a contact in this manner 4 2 2 Rename Contact You can rename a contact in your contact list by right clicking the contact in the Services panel and selecting Rename Contact then entering a new name for the contact This only changes the name displayed for the contact in the Services Panel 74 CHAPTER 4 COLLABORATION PRO ONLY Rename Contact x Y Name for myaccount biomatters dyndns org J J PO co Figure 4 5 Rename Contact dialog box 4 2 3 Remove Contact If you no longer wish to share documents with a contact you can remove that contact by right clicking the contact in the Services panel and selecting Remove Contact This deletes you from their contact list as well If you find that a contact has disappeared from your list this may be the reason 4 3 Sharing Documents Select one of your local folders Select Share Folder from the File menu Alternatively right click on a local folder and select the same option e If you share a folder all documents in that folder are shared e If you share a folder all sub folders of that folder are shared e If you share a folder it is available to all your contacts 4 4 Searching Contacts You can search each of your contacts individually or you can search all the contacts in an acco
17. a one in a thousand 1073 Consensus This option is available when viewing alignments When checked the viewer displays the consensus sequence with the aligned sequences The consensus sequences has the same length and shows which residues are conserved are always the same and which residues are variable Basically a consensus is constructed by taking the most frequent residue at each site position with some special considerations for ties and gaps Ties in a DNA alignment are resolved by taking the appropriate IUPAC nucleotide ambiguity code i e R for A or G etc A tie in a protein alignment is indicated by the general ambiguity symbol X no gaps in consensus When this box is checked gaps are not counted and the consensus sequences does not contains any gaps Majority consensus When this box is checked only the major character is displayed in the con sensus and ambiguity codes only arise in the case of ties However when this box is unchecked the relative frequencies of the residues is ignored i e a Strict consensus is performed so that if there is any polymorphism it is recognized For example a site containing 4 G s and one A would have an R as the consensus This generally implies ignoring gaps since every position normally has at least one non gap residue Zoom options These are a few options that can be turned on or off Auto zoom to selection If this option is turned on when you select a range of sequence residu
18. amino acid occurs with a frequency of 5 in protein sequences This model also assumes that all nucleotide substitutions occur at equal rates and all amino acid replacements occur at equal rates HKY The HKY model 8 assumes every base has a different equilibrium base frequency and also assumes that transitions evolve at a different rate to the transversions Tamura Nei This model also assumes different equilibrium base frequencies In addition to distinguishing between transitions and transversions it also allows the two types of transitions A gt G and C lt T to have different rates 21 3 8 5 Resampling Bootstrapping and jackknifing Resampling is a statistical technique where a procedure such as phylogenetic tree building is repeated on a series of data sets generated by sampling from an original data set The results of analyzing the sampled data sets are then combined to generate summary information about the original data set In the context of tree building resampling involves generating a series of sequence alignments by sampling columns from the original sequence alignment Each of these alignments known as pseudoreplicates is then used to build an individual phylogenetic tree A consensus tree is constructed from by combining information from the set of generated trees providing an estimate for the level of support for each clade in the final consensus tree 4 Bootstrapping is the statistical method of resampl
19. are described below 64 CHAPTER 3 DATA PROCESSING Branch length A measure of the amount of divergence between two nodes in the tree Branch lengths are usually expressed in units of substitutions per site of the sequence alignment Nodes or internal nodes of a tree represent the inferred common ancestors of the sequences that are grouped under them Tips or leaves of a tree represent the sequences used to construct the tree Taxonomic units These can be species genes or individuals associated with the tips of the tree A phylogenetic tree can be rooted or unrooted A rooted tree consists of a root or the common ancestor for all the taxonomic units of the tree An unrooted tree is one that does not show the position of the root An unrooted tree can be rooted by adding an outgroup a species that is distantly related to all the taxonomic units in the tree A common format for representing phylogenetic trees is the Newick format 12 3 8 2 Neighbor joining In this method neighbors are defined as a pair of leaves with one node connecting them The principle of this method is to find pairs of leaves that minimize the total branch length at each stage of clustering starting with a star like tree The branch lengths and an unrooted tree topology can quickly be obtained by using this method without assuming a molecular clock 18 3 8 3 UPGMA This clustering method is based on the assumption of a molecular clock 14 It is appropriate
20. are shown in bold The agent is currently searching e Disabled The agent will not perform any searches e Service unavailable The agent cannot find the database it is scheduled to search This will happen if the database plugin has been uninstalled or if for example the Collabora tion contact is offline currently e No search scheduled The agent is enabled but doesn t have a search scheduled To correct this click the Run now button in the agent dialog to have it search immediately and schedule a new search Deliver To This names the destination folder for the downloaded documents This is usually your Local Documents or one of your local folders Note If you close Geneious while an agent is running it will stop in mid search It will resume searching when Geneious is restarted Also all downloaded files are stored in the destination folder and are marked unread until viewed for the first time 2 4 3 Manipulating an agent Once an agent has been set up it can be disabled enabled edited deleted and run All these options are available from within the Agents dialog e Enable or disable an agent by clicking the check box in the Enable column e Run Now Cause the agent to search immediately e Cancel If the agent is currently searching this can be clicked to stop the search e Edit Click this to change an agent s database search criteria destination or search in terval e De
21. by either right clicking on Collaboration in the Services Panel and clicking Add New Account in the popup menu or by selecting the same option from menu at the top 69 70 CHAPTER 4 COLLABORATION PRO ONLY 4 1 1 Add New Account In this dialog you are given the options of creating a new account on the server or entering the details for an existing account In most cases you will be creating a new account but there may be occasions when you need to re enter the details of an existing account If you choose to create a new account Geneious will attempt to automatically register your account on the server at the end of this process 7 Add New Account my xj Create a new account on the server This account already exists just connect Username Password Confirm password 7 Connect every time I run Geneious gt More Options Cancel Figure 4 1 Add New Account dialog box Choose a username and password now Enter your password twice for a new account If you want this account to connect to the server every time you start Geneious check the checkbox labelled Connect every time I run Geneious More Options You can change some of the defaults for new and exiting accounts e Account Name is the name displayed in the Services Panel for this account It defaults to your username if nothing is entered Server is the server your account connects to Jabber Service Name is required by some other
22. cost Enter the desired gap costs for the alignment e Free end gaps Select this option to avoid penalizing gaps at either end of the alignment See details in the Pairwise Alignment section above e Preserve original sequence order Select this option to have the order of the sequences in the table preserved so that the alignment contains the sequences in the same order e Additional options Any additional parameters accepted by the ClustalW command line program can be entered here Refer to the ClustalW manual for a description of the avail able parameters After entering the desired options click OK and ClustalW will be called to align the selected sequences or alignment Once complete a new alignment document will be generated with the result as detailed previously 3 8 Building Phylogenetic trees Geneious provides some basic phylogenetic tree reconstruction algorithms for a preliminary in vestigation of relationships between newly acquired sequences For more sophisticated meth ods of phylogenetic reconstruction such as Maximum Likelihood and Bayesian MCMC we recommend specialist software such as PAUP 20 and MRBAYES 17 Geneious implements the Neighbor joining 18 and UPGMA 14 methods of tree reconstruc tion 3 8 1 Phylogenetic tree representation A phylogenetic tree describes the evolutionary relationships amongst a set of sequences They have a few commonly associated terms that are depicted in Figure 2 16 and
23. gt 10007 Australobius 1815 nt e Pi Figure 2 13 A view of dotplot of two sequences in Geneious 2 7 3 3D structure viewer The 3D structure viewer was introduced in Geneious 1 0 Figure 2 14 3D structures can be obtained by searching NCBI s Structure database from within Geneious or by importing 3D structure files such as PDB files but other formats are supported as well from your hard drive To view the molecule from another angle just click on the molecule and drag the mouse to rotate it If you would like to change the zoom level of the molecule just hold the shift key and the mouse button and then drag up and down to zoom out and zoom in Another way is to use the scroll button on your mouse Scrolling down enlarges the image and scrolling upwards shrinks it Under Windows and Linux you can also move the molecule parallel to the viewing plane while pressing Ctrl Alt left mouse button This is currently not possible under Mac OS There are a several viewing options available for 3D structures Show atoms This shows the atoms on the molecule You can use the Size option to increase 2 7 DOCUMENT VIEWERS IN GENEIOUS 45 or decrease the size of the atoms Show bonds This shows the bonds between the atoms of the molecule Show ribbons This option displays the secondary structure of the molecule in the form of rib bons This can be viewed only if the necessary information is available Show hydr
24. methods The most popular and time efficient method of multiple sequence alignment is progressive pairwise alignment The idea is very simple At each step a pairwise alignment is performed In the first step two sequences are selected and aligned The pairwise alignment is added to the mix and the two sequences are removed In subsequent steps one of three things can happen e Another pair of sequences is aligned e A sequence is aligned with one of the intermediate alignments e A pair of intermediate alignments is aligned This process is repeated until a single alignment containing all of the sequences remains Feng amp Doolittle were the first to describe progressive pairwise alignment 5 Their algorithm used a guide tree to choose which pair of sequences alignments to align at each step Many variations of the progressive pairwise alignment algorithm exist including the one used in the popular alignment software ClustalX 22 3 6 2 Multiple sequence alignment in Geneious Multiple sequence alignment in Geneious is done using progressive pairwise alignment The neighbor joining method of tree building is used to create the guide tree As progressive pairwise alignment proceeds via a series of pairwise alignments this function in Geneious has all the standard pairwise alignment options In addition Geneious also has the option of refining the multiple sequence alignment once it is done Refining an alignment in volves removing
25. of the residue position number above the sequence residues e Show space every 10 residues If you are zoomed in far enough to be able to see individual residues then an extra white space can be seen every 10 residues when this option is selected e Wrap sequence This wraps the sequences in the viewing area A shortcut is to click the layout check box without expanding it e Wrap on 10 residue boundaries This is automatically turned on if the wrap sequence option is on and will force the sequence wrapping to occur in multiples of 10 nucleotides or amino acids e Show sequence and graph names Show or hide sequence and graph names inside the se quence viewer panel 2 7 DOCUMENT VIEWERS IN GENEIOUS 39 Graphs This option is visible when viewing protein sequences chromatogram traces multiple se quences or sequence alignments Turn this option on by clicking the Graph checkbox and the graph s will be displayed below the sequence s A number of graphs are available Similarity This is available for sequence alignments and when more than one nucleotide protein sequence are displayed It displays the similarity across all sequences for every position Green means that the residue at the position is the same across all sequences Yellow is for less than complete similarity and red refers to very low similarity for the given position Figure 2 11 es Extract E Reverse Complement Translate P Edit
26. oxide This is useful for performing generic searches You can also place the asterisk in the middle of the word Please note Wild card searches only work on searches in the local folders in Geneious 2 3 SEARCHING DATABASES AND LOCAL DOCUMENTS USING GENEIOUS 23 2 3 2 Search panel Searching has been designed to be as user friendly as possible To search select the Search button from the toolbar to activate search For non local folders search will be on by default and cannot be closed This applies to NCBI and EMBL databases For local folders search is off by default When search is first activated the document table will be emptied to indicate no results have been found To return to browsing click the Search button again or press the Escape key while the cursor is in the search text field To initiate a search enter the desired search term s in the text field and press enter or click the adjacent Search button Once a search starts the results will appear in the document table as they are found The Search button changes to a Cancel button while a search is in progress and this may be clicked at any time to terminate the search Feedback on a search progress is presented in the status bar directly below the toolbar immunodeficiency Search More Options Name Summary R Ed NC_001802 Human immunodeficiency virus 1 complete genome Ed NC_004455 Simian immunodeficiency virus 2 comp
27. sequences from the alignment one at a time and then realigning the removed 62 CHAPTER 3 DATA PROCESSING sequence to a profile of the remaining sequences The number of times each sequence is re aligned is determined by the refinement iterations option in the multiple alignment window The resulting alignment is placed in the folder containing the sequences aligned In some cases building a guide tree can take a long time since it requires making a pairwise alignment between each pair of sequences The build guide tree via alignment option may speed this part by taking a different route First make a progressive multiple alignment using a random ordering and use that alignment to build the guide tree Notice that while this typically speeds up the process that may not be the case when the sequences are very distant genetically 7 Alignment x Select alignment type Geneious Alignment ClustalW Cost matrix Blosum z v Gap open penalty A Gap extension penalty EEC Alignment type Global alignment y Refinement options Refinement iterations 2 JV build guide tree via alignment Faster Cancel Figure 3 7 The multiple alignment window 3 7 Sequence alignment using ClustalW pro only ClustalW is a widely used program for performing sequence alignment 23 22 If you have ClustalW installed your computer Geneious pro allows you to run ClustalW directly from inside the program without having to ex
28. service of the U S National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals This archive of biomed ical articles dates back to the 1950s PubMed includes links to full text articles and other related resources with the exception of those journals that need licenses to access their most recent issues Entrez Taxonomy This database contains the names of all organisms that are represented in the NCBI genetic database Each organism must be represented by at least one nucleotide or protein sequence UniProt This database is a comprehensive catalogue of protein data It includes protein se quences and functions from Swiss Prot TrEMBL and PIR It has three main components each optimized for a particular purpose The scope and depth of these databases make them critical information sources for molecu lar biologists and bioinformaticians alike However a library is only as good as its librarian Geneious is your librarian allowing you to search for filter and store only the data that you care about 2 2 2 Accessing NCBI BLAST through Geneious BLAST 1 stands for Basic Local Alignment Search Tool It allows you to query the NCBI sequence databases with a sequence in order to find entries in the public database that contain similar sequences When BLAST ing you are able to specify either nucleotide or protein sequences and nucleotide sequences can be either DNA or RNA sequences
29. the action menu Mac OS X or by holding down the control button and clicking Mac OS X Also in Mac OS X you can also use the plus and minus buttons located at the bottom of the service panel 30 CHAPTER 2 DATA HANDLING to create and delete folders 2 5 1 Transferring data It is quick and easy to transfer data to your local folders from either a Geneious database search or from your computer s hard drive Please check you have already set up your destination folders before continuing Moving documents from Geneious searches to your Local folders There are a number of ways to do this Drag and drop This is quickest and easiest Select the documents that you want to move Then while holding the mouse button down drag them over to the desired folder and release If you dragged documents from one local folder to another this action will move the documents so that a copy of the document is not left in the original location In external databases such as NCBI the documents will be copied leaving one in its original location Drag and copy While dragging a document over to your folder hold the Ctrl key Alt key on Maje s down This places a copy of the document in the target folder while leaving a copy in the original location This is useful if you want copies in different folders The Edit menu Select the document and then open the Edit menu on the menu bar Click on Cut Ctrl X Command X or Copy C
30. the manual 1 2 2 The Document Table The Document Table displays summaries of downloaded data such as DNA sequences protein sequences journal articles sequence alignments and trees By clicking on the search icon you can search data for text or by sequence similarity BLAST Data can also be filtered using the Filter box located at the right side of the toolbar 1 2 3 The Document Viewer Panel The Document Viewer Panel is where sequences alignments trees and journal article abstracts can be shown graphically or as plain text This panel also offers various options while visu alizing protein and nucleotide sequences These options include zooming color and layout selection and annotations When viewing trees there are additional options for branch and leaf labeling and controlling tree layout When viewing journal articles this panel includes a direct link to Google Scholar All these options are displayed on the right hand side of the panel Figure 1 3 exact El reverse complement BP Transiare 2 edn ES arnoracon E Saw a Ps Bc AAA Estimating mutation parameters population history and genealogy simultaneously pssie 2 gt Layout from temporally spaced sequence data Whale y Formatting JACGATCGATC GATCGATCGA TCGACTGACT GACTAGCTAC GATCGATCGA Alexei Drummond Geoff K Nicholls Alen G Rodrigo amp Wiremu Solomon School of Biological Sciences University of Aucidend 1001 Auckland New Zeeland
31. you have the choices Jukes Cantor HKY and Tamura Nei If you are building a tree from amino acid sequences you only have the option of Jukes Cantor distance correction Tree building method There are two methods under this option Neighbor joining 18 and UPGMA 14 Consensus method via resampling Check this box to build a consensus tree using resampling of sequence alignment data Resampling method Either bootstrapping or jackknifing can be performed when resampling columns of the sequence alignment 3 9 BLAST 67 Number of samples The number of alignments and trees to generate while resampling and building a consensus tree A value of at least 100 is recommended Support threshold This is used to decide which monophyletic clades to include in the consensus tree after comparing all the trees in the original set as defined below Resampling results in a set of trees which we will refer to as the original set of trees for the definitions that follow A 100 support threshold results in a Strict consensus tree which is a tree where the included clades are those that are present in all the trees of the original set A 50 threshold results in a Majority rule consensus tree that includes only those clades that are present in the majority of the trees in the original set A threshold less that 50 gives rise to a Greedy consensus tree In constructing a Greedy consensus tree cla
32. ABOUT BIOMATTERS i NTA siomatters BIOMATTERS vaww biomatters com CREATORS OF geneous Research in a flash Welcome to Biomatters Biomatters develops unique easy to use and essential bioinformatics software that speeds up and simplifies research for all molecular biologists and biochemists Introducing Geneious Geneious is a self organizing automatically updating library of genomic and genetic data that provides a fully integrated Read about Biomatters Q READ BLOG visually advanced toolset for Sequence alignment and phylogenetics Sequence analysis e BLAST Protein structure viewing NCBI EMBL Pubmed auto find amp More Geneious Hits No1 on Apple website 26 Apr 2006 Geneious 1 0 hit the No 1 spot as the most downloaded software on Apple s Math amp Science website just two days after its launch The high download rate matches the MORE Find out more about Geneious Bioinformatics finally gets user friendly 24 Apr 2006 If you can use email you can use Geneious 1 0 Any scientist who uses email can now embark on novel research once considered advanced bioinformatics Announcing the launch of Geneious MORE g Download Geneious 1 2 1 Click the link above to download the Geneious application for free today Top EU scientist visits Biomatters 22 Mar 2006 Dr Gerton Lunter one of Europe s leading exp
33. G eee A AR AA BE eS 72 La BOE LOCOS gt e Me eed Pee ee eR EEE ERY 74 Ad Searching IOI ke ge oe eel ee OPUS OWS ERE ES 74 Chapter 1 Getting Started By the end if this chapter you should e Be able to download install and upgrade Geneious e Be able to import Notes and Documents from earlier versions of Geneious e Be familiar with the layout of Geneious e Be able to solve connection problems 1 1 Downloading amp Installing Geneious Geneious is free software that can be downloaded from http www geneious com The panel on the right hand side of the Geneious home page Figure 1 1 allows users to down load Geneious onto three operating systems Windows Mac OS X or Linux Make sure your system meets the requirements before downloading Geneious Click on the operating system to take you to the Download Geneious page Follow the in structions on the page to download and save Geneious It is often easiest to save the program to your desktop Once Geneious is saved double left click on the Geneious icon to start installing the program While this is happening you will be prompted for a location to install Geneious Please check that you are satisfied with the location before continuing CHAPTER 1 GETTING STARTED Welcome to Biomatters Biomatters Mozilla Firefox Ele Edit View Go Bookmarks Tools Help a gt gt 3 2 A O http www biomatters com Getting Started E Latest Headines
34. Geneious 2 0 Biomatters Ltd August 2 2006 Contents 1 Getting Started 5 1 1 Downloading amp Installing Geneious 2 242484 ei cirios 5 1 2 Using Geneious t r the first ime ke ca cs REDRESS REESE ESS 7 L CORON TA e a ee O eee Bees oS 10 2 Data handling 13 21 Imports and exporting data se et eses n e eee eed 13 22 Acquiring data irom publie databases 2 0 52 eet mesos sata see De h 18 2 3 Searching databases and local documents using Geneious 22 24 Apen A Let eae Pona eee AA OLE e de Ea 26 29 Storing data in Genei us oe s sssrini aaa EE EYES EHR ERS ERS 29 26 Panelsin Geneious i o iia irradia EEEa 32 2 7 Document Viewers in Geneious aooaa a 37 20 Pelens o oea o as AA a eee a 48 3 Data Processing 51 al PASTEN eee arene ke Bae ORK OSs OLE R ee E EA 51 we ii each Ged koa Riad kale Copa dS Hed See ad wa ead es 56 23 DOUE dila s eek eee hehehe Oe AA ACA E OE OG OES HS 57 Be NS 2 2b eRe Pha eee FES ERES ODES ARES CREE BOGOR 57 3 5 Pairwise sequence alignments oe oa rl OSE Ee ERE SERS ERY 58 CONTENTS 36 Multiple sequence alignments cis ec re EES Ye OA ee ee 60 3 7 Sequence alignment using ClustalW pro only o o ooo 62 30 Building Fhylogenetic rees jac gk be AA A AAA 63 Oe BLAST Is oe e OE PS AAA oe eee e 67 310 Resul o Bo o qk ae Sk hw A EE AE Oe ee SES eS 67 Collaboration pro only 69 4l Managing Your ALCOUIS lt lt lt cras madera bo we bi sania mak k rede sh 69 2 INIA Your COA
35. Jabber service providers such as Google Talk e Port Number for Jabber servers running on a non standard port 4 1 MANAGING YOUR ACCOUNTS Add New Account alk geneious com po eee PO Ej A fakgeneicus com E A o i Figure 4 2 Add New Account dialog box with More Options 71 72 CHAPTER 4 COLLABORATION PRO ONLY 4 1 2 Edit Account Details Select your account in the Services Panel and this option from the menu Or right click on your account and select it from the popup menu This option is only available when your account is not connected This dialog has nearly all the same fields as the Add New Account dialog Remember that if you change details such as your username or password you may not be able to connect to your account 4 1 3 Connect Disconnect Connect to or disconnect from the server by right clicking on your account or selecting your account in the Services Panel and choosing that option from the menu at the top 4 14 Delete Account You can delete an account from Geneious by right clicking on your account or selecting your account in the Services Panel an choosing that option from the menu at the top This does not delete the account on the server 4 2 Managing Your Contacts Once you have an account and are connected you can start adding contacts You will not be able to add contacts while an account is disconnected 4 2 1 Add Contact Select your account in the Ser
36. TTANGXKEYYODKNGGNFFKLREDWWTANRETVWKAITCGA seq3 KRIYKKIFKEIHSGLSTKNGVKDRYON DGDNYFOLREDWWTANRSTVWKALTCSD seq4 SORHYKD DGGNYFOLREDWWTANRHTVWEAITCSA seg NVAALTLKTRYEK DGONFYOLREDWWTANRATIWEAITCSA seq6 FSKNIX OTEELODEWLLEARYKD TDNYYELRERWWIENRHTVWEALTCEA seq7 KELWEALTCSR seql GGGKYERNTCDG GONPTETONNCRCIG ATVPTYFDYVPOYLRWSDE seq2 P GDASYFHATCDSGDGRGGAQAPHKOCRODG ANVVPTYFDYVPOFLRWPEE seq3 KLSNASYFRATC SDGOSGAQANNYCRONGDKPDDDKP NTDPPTYEDYVPOYLRWSEE seg4 DKGNA YFRRTCNSADGKSOSQARNOCRC KDENGKN ADOVPTYFDYVPQYLRWSEE seq5 DKGNA YFRATCNSADGKSOSQARNOCRC KDENGXN ADOVPTYFDYVPOYLRWSEE seg6 P GNAQYFRNACS EGKTATKGKCRCISGDPD PTYFDYVPOYLRWSEE seg P KGANYFVYKLD RPKFSSDRCGHNYNGDP LINLDYVPOYLRWSDE EndNote 8 0 XML format EndNote is a popular reference and bibliography manager EndNote lets you search for journal articles online import citations perform searches on your own notes and insert references into documents It also generates a bibliography in different styles Geneious can interoperate with EndNote using Endnote s XML Extensible Markup Language file format to export and import its files FASTA format The FASTA file format is commonly used by many programs and tools including BLAST 1 T Coffee 16 and ClustalX 22 Each sequence in a FASTA file has a header line beginning with a gt followed by a number of lines containing the raw protein or DNA sequence d
37. ach field type For ex 54 CHAPTER 3 DATA PROCESSING ample numbers have numerical constraints is greater than is less than is greater or equal to and is less or equal to These can be changed to suit The constraints for each field can be viewed by clicking the View Constraints button next to the field This will show a pop up menu with the constraints you have chosen 3 3 x Existing Note Types Note Person Source Date of birth HE View Gonstraints Sex View Constraints Height View Constraints Create Note Type Delete Note Type Edit Note Type Add Note Done Figure 3 3 Viewing constraints for a field Using Note Types The main purpose of Notes is to add user defined information to Geneious documents How ever Notes and Note Types can be searched for and filtered as well Also columns can be ordered according to the values of an added Note Searching Once a Note Type is defined and a Note of that type added it is automatically added to the standard search fields These are listed under the Advanced Search options in the Document Table From then on you can use them to search your Local Documents If you have more than one Field Type for a Note Type they will both appear as searchable fields in the search criteria Filtering Note values can be used to filter the documents being viewed To do so type a value of your Note Type into the Filter Box in the
38. al aln Alignments ClustalX Endnote 8 0 XML xml Journal article references Endnote Journal article websites Fasta fasta fas etc Sequences alignments PAUP ClustalX BLAST FASTA Geneious xml geneious Preferences databases Geneious Newick tre tree etc Phylogenetic trees PHYLIP Tree Puzzle PAUP ClustalX Nexus nxs nex Trees Alignments PAUP Mesquite MrBayes and MacClade PileUp msf Alignments pileup gcg Rich Sequence Format rsf Sequences alignments GCGs NetFetch DNA Strider str sequence DNA Strider Mac program ApE PDB pdb 3D Protein structures SP3 SP2 SPARKS Protein Data Bank PDF pdf Documents presentations Adobe Writer BIEX Miktex Raw sequence text seq Sequences Any file that contains only a sequence Sequence Chromatograms abl scf Raw Sequencing trace and sequence Sequencing machines CLUSTAL format The Clustal format is used by ClustalW 23 and ClustalX 22 two well known multiple se quence alignment programs Clustal format files are used to store multiple sequence alignments and contain the word clustal at the beginning An example Clustal file CLUSTAL W 1 74 multiple sequence alignment 2 1 IMPORTING AND EXPORTING DATA 15 seql KSKERYKDENGGNYFOLREDWWDANRETVWKAITCNA seq2 YEGL
39. ally used to create the matrix BLO SUM matrices with higher numbers are more suitable for aligning closely related sequences When aligning protein sequences in Geneious a number of BLOSUM and PAM matrices are available 3 5 2 Algorithms for pairwise alignments Once a scoring system has been chosen we need an algorithm to find the optimal alignment of two sequences This is done by inserting gaps in order to maximize the alignment score If the sequences are related along their entire sequence a global alignment is appropriate However if the relatedness of the sequences is unknown or they are expected to share only small regions of similarity such as a common domain then a local alignment is more appropriate An efficient algorithm for global alignment was described by Needleman and Wunsch 15 and their algorithms was later extended by Gotoh to model gaps more accurately 6 For local alignments the Smith Waterman algorithm 19 is the most commonly used See the references provided for further information on these algorithms 3 5 3 Pairwise alignment in Geneious A dotplot is a comparison of two sequences A pairwise alignment is another such comparison with the aim of identifying which regions of two sequences are related by common ancestry and which regions of the sequences have been subjected to insertions deletions and substitu tions 60 CHAPTER 3 DATA PROCESSING Alignment options The options available for the alignme
40. an option to perform the alignment using ClustalW an independent and widely used alignment program Figure 1 4 The Help Panel 1 2 5 The Toolbar The Toolbar displays nine large icons Back Forward Search Agents Add Note Sort Alignment Tree Help and a drop down arrow in between the Back and Forward icons providing quick access to previous views The Toolbar also has a Filter box at the far right The Search icon is available when local documents are selected The Add Note icon is available when one or more documents are selected The Sort icon is available when exactly one sequence is selected Sorting is done by BLAST ing 2 5 2 the sequence against all other sequences in the folder and ordering according based on E values The Alignment icon only becomes available when two or more protein nucleotide sequences or alignments are selected in the Document Table The Tree icon becomes available when an alignment or a set of sequences is selected The toolbar also allows the user to hide icons when they are not in use Figure 1 5 To hide the icons right click anywhere on the Toolbar to see a list of the icons Then scroll down to the icon you want to hide and left click The tick check 10 CHAPTER 1 GETTING STARTED beside the icon will disappear and the icon will disappear from the Toolbar To make the icons reappear follow the a
41. and drag it to the desired horizontal position Choose columns to show The visible columns can be changed by right clicking Ctrl Click on MacOS on any column header or click the small header button in the top right corner of the table This gives a popup menu with a list of all the available columns Clicking on a column will show hide it Your preference is remembered so if you hide a column it will remain hidden in all areas of the program until you show it again Note If a Note is added to a document refer to the section on Adding Notes for more in formation a Note column is added to the end of the existing Document table Also when accessing BLAST 1 in Geneious the Document Table has additional columns related to the BLAST search 2 6 3 The Document Viewer Panel The Document Viewer Panel shows the contents of any document clicked on in the Document Table To view large documents it is sometimes better to double click on them This opens a view in a new window In the document viewer panel there are two tabs that are common to most types of documents Text view and Notes Text view shows the document s information in text format The exception to this rule occurs with PDF documents where the user needs to either click the View Document button or double click to view it The Notes tab only appears if the user has added notes to the document Some document types such as sequences trees and structures ha
42. are deposited in the currently selected folder If no local folder is selected then you will be prompted for a local folder This applies to sequence alignments phylo genetic trees sequence translations reverse complements and extraction of sequences Once 68 CHAPTER 3 DATA PROCESSING generated analysis results can be dragged to another location if desired Chapter 4 Collaboration pro only Collaboration allows Geneious users to share the products of their research and work with each other It uses an open internet protocol called Jabber to move documents across the internet It can work with any existing Jabber service such as Google Talk but we recommend using the Geneious default talk geneious com If you have the knowledge to run and manage your own Jabber server we recommend us ing Wildfire from Jive Software http www jivesoftware org wildfire which is available for free under the GNU General Public License http www gnu org copyleft gpl html Collaboration is only available in Geneious pro This chapter shows you how to e Create a new collaboration account e Search for and add contacts to your account e Share local folders with your contacts e Search your contacts as you would an online database 4 1 Managing Your Accounts When you start Geneious you will see the empty Collaboration service in the Services Panel and the Collaboration menu at the top You can open the Add New Account dialog
43. ask simple through several user friendly tools such as Notes Filtering Text Matching and Similarity Searching 3 1 1 Notes Add Note is a unique feature offered by Geneious Any Notes that you add can be treated as user defined fields for use in sorting searching and filtering your documents 51 52 Where can I add Notes CHAPTER 3 DATA PROCESSING The Add Note function can be used to add notes to all the data types that Geneious can handle including molecular sequences phylogenetic trees and journal articles How do I add Notes There are 3 ways to open the Add Note dialog 1 Right click on a document Select a document and right click Ctrl click for Macs to open an options menu Scroll down to Note and select it 2 Through the Toolbar Click the Note icon on the Toolbar 3 From the Tools menu Click on the Tools menu on the Toolbar Scroll down to Add Note and click 008 Existing Note Types Note Person Protein Size d Create Note Type Delete Note Type Edit Note Type Add Note Protein Size Protein Size View Constraints Figure 3 1 The Add Note Menu The top left panel lists the existing Notes types Click on a Note type and add your note For example if you choose to add a note of the type Person you could add your name to record that the sequence was produced by you 3 1 DATA FILTERING 53 Creating Note Types Geneiou
44. ata The sequence data may span multiple lines and these sequence may contain gap characters An empty line may or may not separate consecutive sequences Here is an example of three sequences in FASTA format DNA Protein Aligned DNA gt Orangutan ATGGCTTGTGGTCTGGTCGCCAGCAACCTGAATCTCAAACCTGGAGAGTGCCTTCGAGTG gt gi 532319 pir TVFV2E TVEV2E envelope protein ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT QIWOK gt Chicken 16 CHAPTER 2 DATA HANDLING CTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA CTGT CATCTTAA Geneious format The Geneious format can be used to store all your local documents note types and program preferences A file in Geneious format will usually have a geneious extension or a xml extension This format is useful for sharing documents with other Geneious users and backing up your Geneious data Newick format The Newick format is commonly used to represent phylogenetic trees such as those inferred from multiple sequence alignments Newick trees use pairs of parentheses to group related taxa separated by a comma Some trees include numbers branch lengths that indicate the distance on the evolutionary tree from that taxa to its most recent ancestor If these branch lengths are present they are prefixed with a colon The Newick format is produced by pro grams such as PHYLIP PAUP ClustalW 23 ClustalX 22 Tree Puzzle 7 and PROTML Geneious is also able to read trees in Ne
45. atenate sequences or sequence alignments A viewer which shows a simply text view of any document type Provides methods for building trees from alignments fox gt Cancel Apply Restore defaults Author s Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Andrew Rambaut Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Biomatters Figure 2 18 The plugins preferences in Geneious Version F 1 3 5 1 3 5 3 3 5 1 3 5 0 9 2 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 0 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 s 13 5 1 3 5 1 3 5 1 3 5 1 3 5 1 3 5 A Chapter 3 Data Processing This chapter details the different ways that data can be filtered and analyzed in Geneious By the end of this chapter you should be able to Filter data using the tools in Geneious Know about the advantages of the Add Note function Understand the basic principles of bioinformatics e Perform simple bioinformatics analyses with Geneious 3 1 Data Filtering The public bioinformatics databases are large and growing rapidly and often contain redun dant data and partial matches This makes it extremely difficult to locate only the most rele vant information Geneious makes this t
46. bles two text fields Proxy host and Proxy port This information is in your browser s connection settings Please see step 3 e Use auto config file This enables one text field called Config file location These details can also be found in your browser s settings 6 Finally set the proxy settings under the General tab to match those in your browser Note If you are using any other browser and cannot find the proxy settings please email us at support geneious com 12 CHAPTER 1 GETTING STARTED Tools Preferences Tools Internet Advanced Options Options Proxies Connection Connections 4 Settings Connection Lan Settings Settings Figure 1 6 Checking browser settings eS Preferences L General Plugins General settings Data Storage Location Users alexei Geneious Search history Mi Check for new versions of Geneious 7 Also check for beta versions of Geneious Connection settings Use browser connection settings A Proxy host Proxy port Config file location Proxy Help ox Cancel Apply Restore defaults Figure 1 7 General Preferences Chapter 2 Data handling Geneious is a one stop shop for handling and managing your bioinformatic data This chapter summarizes the different ways you can use Geneious to acquire update organize store and view your data By the end of this chapter you should be able to e Import Export data from various
47. bove steps in reverse e080 Geneious pro trial 1 3 5 a o gt PB AT 4 Back Forward Search Agents Note Sort Alignment Tree v Show Labels Completed found 23 documents v Large Icons Sources Y Local 32 Jd a v Back gt 185 22 v History DefaultPhylogenyDocumentTest 14 pg 58 v Forward v Hiv 0 v Search nef 40 pg 79 v Agents v NewcastleDisease 1 V Divider 1 lentogenic1 23 pg 164 Y Note p lentogenic2 19 SO Y Sample Documents 0 pg 293923 e 3D Structures 2 a Divider 2 Alignments 82 pg 293925 v Alignment Nucleotide Documents 4 v Tree 5 Protein Documents 2 E 293927 v Divider 3 7 L Y A acres eal 7229463 alo Figure 1 5 The Toolbar 1 2 6 The Menu Bar The Menu Bar has five main menus File Edit Tools Collaboration and Help These are discussed in more detail at the end of Chapter 2 1 3 Troubleshooting 1 3 1 Geneious won t start Geneious has some minimum system requirements It is compatible with the three most com mon operating systems Windows Mac and Linux Check that you have one of the following OS versions before you launch Geneious Operating System System requirements Windows 2000 XP Mac OS X 10 4 Unix Linux 1 3 TROUBLESHOOTING 11 Geneious also needs Java 1 5 to run If you do not have this on your system already please download it from http www geneious com On the download page
48. ce with the right mouse button or by clicking the Options button at the bottom of the Service Panel in Mac OS X 2 6 2 The Documents Table The Document Table displays your search results or your stored documents While search results usually contain documents of a single type a local folder may contain any mixture of documents whether they are sequences publications or other types If you cannot see all of the columns in the document table you may want to close the help panel to make more room 2 6 PANELS IN GENEIOUS File Edit Tools Menu Bar 33 amp gt PETAT fl Tool Bar a Forward e Agents Note Sort Alignment Tree Help alae found 2 documents Sources Help El T Alignment V Include Subfold Search 32 More Options e pa E A ja i ai Tutorial Help gt gt acna 30 nf ebgc 58 Name Summary Re gt Envelope sequences 108 A missing annotation house mouse ger Folder Alig nments 8 Genes 0 E A B o This is your Local Documents service gt Downloaded 336 pf Extracted 52 New he 27 unread E 3D Structures 2 Alignments 7 0 Nucleotide Documents 3 gt Protein Documents 2 gt Tree Documents 2 o Temporary 3 2 unread 8 amp Collaboration Bg strabo richard talk geneious com 5 Emer E Uniprot 5 ncel 5 BLAST blastn blastp blastx j tblastn tblastx oof Genome Nucleo
49. database to search search frequency and the folder you wish the agent to deliver its results to The search frequency may be specified in minutes hours days or weeks You can only use whole numbers Selecting Only get documents created after today will cause the agent to check what docu ments are currently available when the agent is created Then when the agent searches it will only get documents that are new since it was created e g If you have already read all publi cations by a particular author and you want the agent to only get publications released in the future Alternatively you can click the Create Agent button which is available in some advanced search panels This will use the advanced search options you have entered to create the agent The easiest way to organize your search results is to create a new folder and name it appropri ately You can do that by navigating to the parent folder in the Deliver to box and click New Folder or by creating a new folder beforehand 1 Right click for Windows Unix Macs with a 2 button mouse on the Sample Docu ments or Local folders This brings up a popup menu with a New Folder option 2 Create a new folder and name it according to the contents of the search For example type CytB if searching for cytochrome b complex 2 4 AGENTS 27 3 Once created select the new folder You can now select the Create or Create and
50. des are first ordered according to the number of times they appear i e the amount of support they have then the consensus tree is constructed progressively to include all those clades whose support is above the threshold and that are compatible with the tree constructed so far Note The above definitions apply to rooted trees The same principles can be applied to un rooted trees by replacing clades with splits Each branch edge in an unrooted tree corre sponds to a different split of the taxa that label the leaves of this tree 3 9 BLAST BLAST Basic Local Alignment Search Tool is a fast method to search large databases of se quences for a sequences similar to a query sequence 1 Geneious provides access to the NCBI sequence databases via BLAST For more information on BLAST check out http www ncbi nlm nih gov BLAST Data from BLAST are summarized in a way similar to protein and nucleotide sequences and can be viewed in the same way too However data from BLAST have an extra e value table and is a result of searching for a GenBank ID or a string of residues The results of the BLAST are a list of the closest matches to the original query Once you have a set of matches you can use them to perform sequence alignments and build trees the way you do with nucleotide and protein sequences For more detailed information on BLAST refer to section 2 2 2 of this manual 3 10 Results of analysis All analysis results
51. e name of a document No nodes ber of Nodes No tips Number of tips Organism Organism The organism of the sequence PDB name Name in PDE PMID The PubMed ID of the article ublished author abl Sequence Annotations seq Sequence Length Residue lenc Sequence Residues Size Size of the document Summary summ URL A url link to the published a y of a document a Figure 2 6 Searching the local documents on a user defined field Similarity BLAST like searching It is possible to search your local documents not only for text occurrences but by similarity to sequence fragments Click the small arrow at the bottom of the large T to the left of the search dialog select Nucleotide similarity search or Protein similarity search and enter the sequence text Geneious will try to guess the type of search based on the text so that simply entering or pasting a sequence fragment may change the search type automatically The search locates documents containing a similar string of residues and orders them in de creasing order of similarity to the string The ordering is based on calculating an e value for each match You can read more about the e value in subsection 2 2 2 For the search to be successful you need to specify a minimum of 11 nucleotides and 3 amino acids Note that search times depend on the number and size of your sequence documents and so may take a long time t
52. e 6 Transmembrane protein HWLES i l IE US20 gene C source 1 ME Transmembrane region m A EA gene 1 Protein 1 E Show All Hide All me Transmembrane protein HWLF3 ype Protein payout residue 1 gt 342 F gene US20 Ee product Transmembrane protein HWLF3foom Options gt Statistics 342 a Y ns region mn Transmembrane region US20 gene o Transmembrane region Transmembran 290 300 3 320 330 342 488 gt ee Be e A lh rs Cursor before residue 0 Figure 2 12 The annotations options in the sequence viewer The sequence viewer toolbar The top of the sequence viewer panel shows a toolbar containing several actions Some of them operate on a part of a sequence or alignment There are several ways to make such a selection e Mouse dragging Click and hold down the left mouse button at the start position and drag to the end position e Select from annotations When annotations are available click on any annotation to select the annotated residues e Click on sequence name This will select the whole sequence e Select all Use the keyboard shortcut Ctrl A to select everything in the panel The available actions are Extract Extract the selected part of a sequence or alignment into a new document Reverse Complement Reverse sequence direction and replace each base by its complement This is available only for nucleotide sequences Translate Translate DNA into pr
53. ences being compared The dots in a dotplot are determined by two factors stringency and window size The strin gency is the number of matches required in the given window size for a dot to be plotted and it acts as a threshold that determines the sensitivity of the dot plot Reducing the required num ber of matches for a given window size will increase the sensitivity of the dotplot but will also lead to more false positives regions that match due to chance alone If the stringency is set to 3 and the window size to 5 then a pair of 5 base windows that contain 3 or more matching nucleotides will be classified as a match A dot corresponding to the center of the two windows will then be displayed in the dotplot Anything less will be classified as a mismatch and no dot will be drawn 3 4 1 Viewing Dotplots To view a dotplot in Geneious select two nucleotide or protein sequences in the Document Table and select Dotplot Viewer in the Document Viewer Panel see Figure 2 13 For more details on the dotplot viewer and the available options refer to section 2 7 2 58 CHAPTER 3 DATA PROCESSING 3 4 2 Interpreting a Dotplot e Each axis of the plot represents a sequence e A long largely continuous diagonal indicates that the sequences are related along their entire length e Sequences with some limited regions of similarity will display short stretches of diagonal lines e Diagonals on either side of the main diagonal indicate re
54. erts in bioinformatics is Biomatters first distinguished overseas expert in a new program designed to build collaboration between Biomatters and the global bioinformatics MORE Copyright 2005 2006 Biomatters Ltd All rights reserved Made by Cactuslab Powered by Supermodel Figure 1 1 The Geneious home page 1 2 USING GENEIOUS FOR THE FIRST TIME 7 1 1 1 Upgrading to new versions All versions of Geneious from 0 9d onwards will automatically self update and retain all of your data If you are upgrading from 0 9b or earlier please see the section Upgrading from Version 0 9b or earlier 1 2 Using Geneious for the first time Figure 1 2 displays the Geneious window when opened for the first time There are six main panels g Geneious pro File Edit Tools Help a Back Search Agents Note Menu Bar LA La oaea Alignment Tree et Tool Bar ane Completed Found 2 documents Sources Local 0 gt acna 30 gt ebgc 58 D Envelope sequences 108 B f Genes 0 5 Downloaded 336 LO Extracted 52 gt New 29 27 unread Services Panel Sample Documents 0 gt 3D Structures 2 Alignments 7 gt Nucleotide Documents 3 F Protein Documents 2 Tree Documents 2 gt Temporary 3 2 unread S Collaboration Edi strabo richard talk geneious com 5 8 Emel e Uniprot 5 ncer 5 BLAST 2 blastn blastp E blastx 7 tblast
55. es 2 7 DOCUMENT VIEWERS IN GENEIOUS 41 the sequence viewer automatically zooms in or out so that the selected piece fills the entire viewing area A shortcut is to select the zoom options checkbox without expanding it Default zoom level This options allows the user to specify the initial level of zoom when viewing a sequence Please note Geneious automatically restores the previous zoom level and over rides the de fault settings when you return to a sequence that you were previously viewing Statistics This displays some statistics about the sequence being viewed They correspond to the se quence alignment being viewed or the highlighted part of the sequence alignment The length of the sequence or part of the sequence is displayed next to the Statistics option Residue frequencies This section lists the residues for both DNA and amino acid sequences and also for alignments It gives the frequency of each nucleotide or amino acid over the entire length of the sequence including gaps If there are gaps then a second percentage frequency is calculated ignoring gap characters The G C content for nucleotide sequences is shown as well for easy reference The following statistics are available when viewing alignments or multiple sequences Pairwise Similarity The average percent similarity over the alignment This is computed by looking at all pairs of bases at the same column and scoring a hit one when they are ident
56. exei J Drummond Simon Y W Ho Matthew J Phillips amp Andrew PLoS Biol Alexei J Dru 16683862 http bic MA modified cc_cd11_M13F_COS modified cc_cd11_M13F_C05_022 ab1 Length 597 GCTCACGA MA cc_cd11_M13F_C05_022 ab1 cc_cd11_M13F_C05_022 ab1 Length 597 gctsacgatgc MA modified cc_cd12_M13F_DOS modified cc_cd12_M13F_D05_021 ab1 Length 618 GCTSCGATG A Nucleotide alignment 6 Alignment of 2 sequences cc_cd11_M13F_C05_022 ab1 82 8 E New nucleotide sequence New nucleotied sequence A new nucleotide sequence entered ACGATCAC ys 1996YangGeneticsv144p194 1996YangGeneticsv144p1941 pdf tree txt tree txt 4 tips m tree3 txt tree3 txt 1 Trees Figure 2 9 The document table when browsing the local folders Selecting a document in the Document Table will display its details in the Document View Panel Selecting multiple documents will show a view of all the selected documents if they are of similar types eg Selecting two sequences will show both of them side by side in the sequence view There are several ways to select multiple documents e Hold Ctrl Command on Mac OS and click to add the document to the current selection e Hold Shift and click to add the document and all documents between it and your previous selection e On windows the right mouse button can be clicked and held while moving the mouse to easily se
57. he Patent division of GenBank PDB Sequences derived from the 3D structures of proteins from PDB RefSeq NCBI curated non redundant sets of sequences SwissProt Table 2 4 Protein sequence searches in the BLAST databases Database Protein searches env_nr Translations of sequences in env_nt month All new updated GenBank coding region CDS translations PDB SwissProt PIR released in last 30 days nr All non redundant GenBank coding region CDS translations PDB SwissProt PIR PRE pat Protein sequences derived from the Patent division of GenBank PDB Sequences derived from 3D structure Brookhaven PDB RefSeq SwissProt Curated protein sequences information from EMBL Geneious can perform five different kinds of BLAST search e blastp Compares an amino acid query sequence against a protein sequence database e blastn Compares a nucleotide query sequence against a nucleotide sequence database e blastx Compares a nucleotide query sequence translated in all reading frames against a protein sequence database You could use this option to find potential translation prod ucts of an unknown nucleotide sequence 22 CHAPTER 2 DATA HANDLING e tblastn Compares a protein query sequence against a nucleotide sequence database dy namically translated in all reading frames e tblastx Compares the six frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database Please note that the tblastx pr
58. ical divided by the total number of pairs Identical sites The number of sites that are identical across all sequences Annotations Some protein and nucleotide sequences come with annotations and these can be viewed within Geneious sequence viewer In the presence of annotations the options panel includes an An notations check box Figure 2 12 Uncheck the check box to turn off all annotations Individ ual annotation types can be turned on or off by using the check boxes next to them Compress annotations This option reduces the vertical height of the annotations on display This reduces the space occupied by annotations by allowing them to overlap and increases the amount of the sequence displayed on the screen Hide all Show all These buttons can be used to turn off and on all annotations on the sequence 42 CHAPTER 2 DATA HANDLING Extract GF Reverse Complement ES Translate 2 Edit BW Annotation HM Save E Sequence View Text View Notes 549172 Hydropho 549172 Hydropho 549172 549172 549172 Hydropho Hydropho Ja Y Hydropho gt Zoom Level MRNISRARSA CTWISCTSES PCSTSCPPSP AAPTNRERS EPQQRRRPSS SPNRRURGYT TSPCPTRSLY Transmembrane protein WLS Gras US20 gene v Mm Annotations C Compress annotations 80 90 100 110 120 130 140 i h h r d Site 3 Ez YKRRNGAPQR ECAETNATMO AQBANALDES RMEALEWFKK FINWERWYAL FIFQUAFSFG EGSMFWEGFP si
59. ing with replacement To apply bootstrapping in the context of tree building each pseudo replicate is constructed by randomly sampling columns of the original alignment with replacement until an alignment of the same size is obtained 4 66 CHAPTER 3 DATA PROCESSING Jackknifing is a statistical method of numerical resampling based on deleting a portion of the original observations for each pseudo replicate A 50 jackknife randomly deletes half of the columns from the alignment to create each pseudo replicate 3 8 6 Tree building in Geneious Geneious can build a phylogenetic tree for a set of sequences using pairwise genetic distances To build a tree select an alignment or a set of related sequences all DNA or all protein in the Document table and click the Build Tree icon or choose this option from the Tools menu Tree from non aligned sequences x Tree Alignment Options Cost matrix 51 similarity 5 0 3 0 yl Gap open penalty ha Gap extension penalty ko o Alignment type Global alignment 0 OC i Tree builder options Genetic Distance Model Jukes Cantor O Tree build Method Jurama sts Outgroup N Cancel Figure 3 8 Tree building options in Geneious If you are building a tree from an alignment the following options are seen in the tree window Genetic distance model This lets the user choose the kind of substitution model used to estimate branch lengths If you are building a tree from DNA sequences
60. labels on the internal nodes of the tree Show branch labels This refers to the branches of the tree Show scale bar This displays a scale bar at the bottom of the tree view to indicate the length of the branches of the tree It has three options Scale range font size and line weight Depending on the option Display can be branch lengths taxon names or node heights You can use Font to change the size of the labels 2 7 5 The Chromatogram viewer The Chromatogram viewer provides a graphical view of a the output of a DNA sequencing machine such as Applied Biosystems 3730 DNA analyzer The raw output of a sequencing machines is known as a trace a graph showing the concentration of each nucleotide against sequence positions The raw trace processed by a Base Calling software which detects peaks in the four traces and assigns the most probable base at more or less even intervals Base calling may also assign a quality measure for each such call typically in terms of the expected probability of making an erroneous call 48 CHAPTER 2 DATA HANDLING Sequence Logo When checked bases letters are drawn in size proportional to call quality where larger implies better quality or smaller chance of error Note that the scale is logarithmic the largest base represents a one in a million 1074 or smaller probability of calling error while half of that represents a probability of only a one in a thousand 107
61. lect a block of documents The popup menu will appear once the mouse is released so the newly selected documents can quickly be manipulated Double clicking a document in the Document Table displays the same view in a separate win dow To view the actions available for any particular document or group of documents right click on a selection of them Ctrl Click on Mac OS X These options vary depending on the type of document The Document Table has some useful features Editing Values can be typed into the columns of the table This is a useful way of editing the information in a document To edit a particular value first click on the document and then click on the column which you want to edit Enter the appropriate new information and press enter Certain columns cannot be edited however eg the NCBI accession number 2 6 PANELS IN GENEIOUS 35 Copying Column values can be copied This is a quick method of extracting searchable infor mation such as an accession number To copy a value right click on it and choose the Copy name option where name is the column name Sorting All columns can be alphabetically numerically or chronologically sorted depending on the data type To sort by a given column click on its header If you have different types of documents in the same folder click on the Icon column to sort then according to their type Rearranging You can reorder the columns to suit Click on the column header
62. lete Delete the agent permanently Any documents retrieved by the agent will re main in your local documents 2 5 STORING DATA IN GENEIOUS 29 Table 2 5 Geneious document types Document type Geneious Icon Nucleotide sequence E Ry Protein sequence 3 Phylogenetic tree fe 3D structure ad A Sequence alignment i Chromatogram Journal articles y PDF Z Other documents 2 5 Storing data in Geneious Geneious can be used to store your documents locally Under the Local folder in the Services Panel you are able to create sub folders to organize and store a variety of document types 2 5 This is also where you can set up special folders to receive documents that are downloaded by a Geneious agent To create a new folder in Geneious select the Local folder or a sub folder icon in the services panel and right click 2 button mouse or Ctrl click 1 button mouse on Mac OS X This will pop up a menu Clicking on New folder opens a dialog that will prompt you to name the folder The named folder is then created as a sub folder of the folder that you originally right clicked on Important Search results will be lost when you exit Geneious unless the downloaded docu ments have been copied or moved to one of your local folders In Geneious you can create new folders rename existing folders delete and export folders All these choices are available by either right clicking on the folder clicking on
63. lete genome Ed NC_001549 Simian immunodeficiency virus complete genome ld NC_003074 Arabidopsis thaliana chromosome 3 complete sequence Ed NC_002305 Salmonella typhi plasmid R27 complete sequence Ed NC_001870 Simian Human immunodeficiency virus complete genome Ed NC_001722 Human immunodeficiency virus 2 complete genome Ed NC_001664 Human herpesvirus 6 complete genome i DB PEGA re f Y n Figure 2 2 The Search tab of the Document Table 2 3 3 Advanced Search options To access advanced search click the More Options button inside the basic search panel To return to basic search click the Fewer Options button Switching between advanced and basic will not clear the search results table This feature provides more search options to select from Geneious allows you to search with a range of criteria however these depend on the database being searched All the fields in the NCBI public databases can be searched in any combination Each database has a specific 24 CHAPTER 2 DATA HANDLING list of fields and it is important to familiarize yourself with these fields to make full use of the Advanced Search The fields available for a search can be found in the left most drop down box after enabling the advanced search options Note When searching the Genome database the documents returned are only summaries To download the whole genome select the summary s of the genome s you would like to download and the click the
64. ll allow full text searches to be performed on the article As well as the abstract and links Geneious also shows the summary of the journal article in BibTex format in a separate tab of the Document Viewer This can be imported directly into a 3 3 SEQUENCE DATA 57 ETFX document when creating a bibliography Alternatively a set of articles in Geneious can be directly exported to an EndNote 8 0 compatible format This is usually done when creating a bibliography for Microsoft Word documents 3 3 Sequence data Basic techniques such as dotplots and pairwise alignments can be used to study the relation ships between two sequences However as the number of sequences increases methods for determining the evolutionary relationships between them become more complicated When analyzing more than two sequences there are some common steps to determine the ancestral relationships between them The next four sections outline the basic tools for prelim inary sequence analysis dot plots sequence alignment and phylogenetic tree building 3 4 Dotplots A dotplot compares two sequences against each other and helps identify similar regions 13 Using this tool it can be determined whether a similarity between the two sequences is global present from start to end or local present in patches The dotplot uses a window of comparison to determine the level of similarity between every pair of sub sequences of length window size in the two sequ
65. n 7 tblastx E Genome B Nucleotide B PopSet e Protein 2 PubMed Structure e Taxonomy unread jad E T Alignment 7 Include Subfolders 32 More Options 5 Name Summary r bicnmentof 2csquences house mouse ger 2 Folder Alignments Document Table Tutorial Help A missing annotation A env alignment AB234101 1 AB This is your Local Documents service You can drag and drop articles and sequences that you find in external databases for example NCBI into this folder for future reference Help Panel Right click on this folder and select Share Folder to allow your contacts to search it over the Collaboration service If you share a folder its sub folders are always also shared Any folders you share can be searched by all your contacts R m fl Sequence View Text View Obras Reverse C gT Edt p Annotation Ps 9 l 10 20 ig la consensus GEGURACUEN GANGEAGEGA ctEcECHCA cH AB234107 1 fe senn ss Document Viewer a Panel a CRRA ie Y ssidue 85 ungapped residue 85 J Figure 1 2 The main window in Geneious 8 CHAPTER 1 GETTING STARTED 1 2 1 The Services Panel The Services Panel contains the services and functions Geneious offers These include your local documents including sample documents EMBL and NCBI links and Collaboration All these services will be described in detail later in
66. n or off e Large Icons Switch between large and small icons e A list of all available toolbar buttons Selecting deselecting buttons will show hide the buttons in the toolbar Note Below the Toolbar there is a grey status bar This bar displays the status of the cur rently selected service For example when you are running a search it displays the number of matches and the time remaining for the search to finish 2 6 6 The Menu bar File Menu This contains some standard File menu items including printing and Exit on Windows On Geneious pro it contains New Sequence which will create a new nucleotide or protein sequence from residues that you can paste or type in It also contains options to create rename delete or share folders and Import Export options Edit Menu Here you will find common editing functions including Cut Copy Paste Delete and Select All These are useful when transferring information from within doc uments to other locations or exporting them This menu also contains Find in Document Find Next and Find Previous options Find can be used to find text or numbers in a se lected document This is useful when looking for annotated regions or a stretch of bases in a sequence This opens a Find Dialog The shortcut to this is Ctrl F Next finds the next match for the text specified in the Find dialog The shortcut keys are F3 or Ctrl G Genei
67. nload it Also check for beta version of Geneious Enable this to also have Geneious alert you when new beta versions are released A beta version is a version that is released before the official release for the purposes of testing It may therefore be less stable than official releases Search History This clears all the previously searched words in Geneious After this the auto completion drop box will be empty Connection settings These are described in the troubleshooting section of the manual 2 8 2 Plugins The Plugins tab Figure 2 18 contains a table of the currently available plugins for Geneious To enable a plugin select the checkbox next to it To disable a plugin deselect the checkbox next to it 50 808 CHAPTER 2 DATA HANDLING Preferences Plugins are optional modules that are not required in order for Geneious to function Plugins may be created by third party software vendors to provide additional features Use this page to enable disable plugins M 3 D structure importer and exp Chromatogram importer and vi RARRARARRARRARRARARRRRRARARRAR RARARA Plugin Name 4 Clustal W importer ClustalW Collaboration beta DNA Strider importer Document Source Viewer Dotplot View EMBL database Endnote FASTA Importer exporter Generate consensus sequence Graphical Sequence View Graphical Tree View JMol MEGA exporter NCBI database New Sequence Newick importer Nexus im
68. nt cost matrix will depend on the kind of sequence e Protein sequences have a choice of PAM 2 and BLOSUM 9 matrices e Nucleotide sequences have choices for a pair of match mismatch costs Some scores distinguish between two types of mismatches transition and transversion Transitions A gt G C gt T generally occur more frequently than transversions Differences in the ratio of transversions and transversions result in various models of substitution When applicable Geneious indicates the target sequence similarity for the alignment scores i e the amount of similarity between the sequences for which those scores are optimal e Both protein and nucleotide pairwise alignments have choices for gap open gap exten sion penalties costs Unlike many alignment programs these values are not restricted to integers in Geneious There is also a check box for free gaps at ends If this is selected gaps at either end of the alignment are not penalized when determining the optimal alignment This is especially useful if you are aligning sequence fragments that overlap slightly in their starting and ending posi tions e g when using two slightly different primer pairs to extract related sequence fragments from different samples x Select alignment type M Geneious Alignment Clustalw Cost matrix Blosum z y Gap open penalty ha Gap extension penalty hoo o ooo Alignment type Global alignment Needleman Wunsch Cancel
69. o complete 2 5 3 Checking and changing the location of your Local folders To check where your Local folders are being stored on your hard drive open the Tools menu in the Menu Bar Click Tools Preferences General Your documents are stored at the location specified by the Data Storage Location field see Figure 2 7 You can change this location by clicking the Browse button and selecting a new location Geneious will remember this new location when you exit 32 CHAPTER 2 DATA HANDLING 608 _ Preferences General _ Plugins General settings Data Storage Location Users alexei Geneious Browse Figure 2 7 Setting the location of your local documents 2 6 Panels in Geneious This section provides more information on each of the panels in Geneious Figure 2 8 2 6 1 The Services Panel The Services Panel shows a tree that concisely displays Geneious functions and your stored documents The plus symbol indicates that a folder contains sub folders A minus indi cates that the folder has been expanded completely and has no sub folders Click these symbols to expand or contract folders Geneious Service Panel allows you to access e Your Local Documents e NCBI databases BLAST 1 Genome Nucleotide PopSet Protein Pubmed Structure and Taxonomy e An EMBL database Uniprot e Your contacts Geneious databases You can view options for any selected servi
70. ogens This option displays the hydrogens attached to the molecule They are shown in white Spin This allows the molecule to spin on a vertical axis for viewing Atom symbols This displays single letter codes for the atoms adjacent to each atom 3 D structure Sequence View Text View Options M Show atoms Size 50 Y Show bonds Y Show ribbons v Show hydrogens LJ Spin __ Atom symbols Hold down the mouse button and drag to rotate Hold down the shift key and mouse button and drag to zoom Figure 2 14 A view of a 3D protein structure in Geneious 2 7 4 Tree viewer The tree viewer provides a graphical view of a phylogenetic tree Figure 2 15 When viewing a tree a number of other view tabs may be available depending on the information at hand The Sequence View tab will be visible if the tree was built from a sequence alignment using Geneious The Text View shows the tree in text format Newick The Notes tab will be present if you have added notes to the tree document There are a number of options for the tree viewer 46 CHAPTER 2 DATA HANDLING a Graphical Tree View Sequence View Text View gt General gt Layout y Formatting Y Transform branches Transform cladogram 43 7 Order branches Ordering increasing vi Show Root Branch A Ya Line Weight 2 gt mM Show Tip Labels v mM Show Node Labels Display Node Heights 5 Font Size
71. ogram cannot be used with the nr database on the BLAST Web page because it is too computationally intensive 2 3 Searching databases and local documents using Geneious Although the above databases are accessible from the NCBI web page Geneious allows you to comfortably search them from your desktop Once you have search results in the Document Table they can be filtered further with the Filter Box in the Toolbar Furthermore once you have started to store your sequences and publications as local documents in Geneious you can also search these local folders using the same easy search interface by clicking on the toolbar search icon which opens the a search dialog 2 3 1 Common search features The following search features are available under both Simple Search and Advanced Search options available by clicking on More Options Matching exact words When you are looking for exact matches to certain words it is important to put them in quotes to reduce the number of incorrect matches This minimizes the number of irrelevant down loads Important You must use quotation marks if and blank spaces are part of your search criteria No quotation marks lead to unreliable results Wild card searches When you are looking for all matches to a partial word use the asterisk For example typing oxi would return matches such as oxidase oxidation oxido reductase and
72. ormation is available PDF format PDF stands for Portable Document Format and is developed and distributed by Adobe Systems http www adobe com It contains the entire description of a document including text fonts graphics colors links and images The advantage of PDF files is that they look the same regardless of the software used to create them Some word processors are able to export a document into PDF format Alternatively Adobe Writer can be used Currently you can use Geneious to read store and open PDF files and future versions will have more options for storing and manipulating PDF Sequence Chromatograms Sequence chromatogram documents contain the results of a sequencing run the trace and a guess at the sequence data base calling Informally the trace is a graph showing the concentration of each nucleotide against sequence positions Base calling software detects peaks in the four traces and assigns the most probable base at more or less even intervals 2 1 3 Where does my imported data go The above formats can be all imported into Geneious from files on your hard drive Geneious also enables you to download certain types of documents directly from public databases such 18 CHAPTER 2 DATA HANDLING as NCBI and EMBL The method used to retrieve a particular piece of data will determine where in Geneious it is stored Data imported from your hard drive This is imported directly into the currently selected local
73. otein Clicking on this choice brings up a list of genetic codes that can be used Choose the appropriate one and click OK This is available only for nucleotide 2 7 DOCUMENT VIEWERS IN GENEIOUS 43 sequences Edit Annotations and Save Editing sequences and alignments To edit sequence s or an alignment click the Edit toolbar button After selecting a residue or a region you can either type in the new contents or use any of the standard editing operation such as Copy Ctrl C Cut Ctrl X Paste Ctrl V and Undo Ctrl Z All operations are under the main Edit menu Selecting a region enables the Annotations button as well which opens an annotation en try dialog Enter an annotation name and select a existing type or type a new one Click on More Options to enter additional properties for that annotation Double click on an existing annotation to edit it or right click Ctrl click on Mac OS X to display a pop up menu to delete annotations You can also copy an annotation from one sequence to another from the pop up menu When editing an alignment it is possible to select a region which may span several sequences and drag it to the left or right Dragging will either move residues over existing gaps or open new gaps when necessary Dragging a selection consisting entirely of gaps moves the gaps to the new location To quickly select a single residue double click on it Triple clicking will select a block of
74. ous then allows you to choose another document and continue searching for the same search word Prev finds the previous match The shortcut keys for this are Ctrl Shift G or Shift F3 2 7 DOCUMENT VIEWERS IN GENEIOUS 37 Tools Menu This contains a list of features such as Note Alignment Tree Viewers and Preferences Click on Viewers to get a list of all the viewers available in Geneious Collaboration Menu pro only This contains actions that can be performed with Collaboration accounts which allow you to share you work with other Geneious users Help Menu This consists of the standard Help options offered by Geneious 2 7 Document Viewers in Geneious 2 7 1 The Sequence and alignment Viewer The Sequence view tab in the Document Viewer panel is available for Nucleotide sequences Protein sequences Alignments and some 3D structure documents The options available are grouped under headings Zoom level Annotations Colors Layout Zoom options and Statistics The presence of these options varies with the kind of sequence data being viewed Extract E Reverse Complement SS Translate i Edit Annotation Save a i 33 66 19 132 165 198 231 64 i i 0 0 1 i q 1 1 AS v _ Zoom Level EXA a 16 AE 1 Cys peroxiredox 1 Cys peroxiredox Y Bl Amnotations O Compress annotations 330 363 396 429 a 5 56 594 627 wv A EXT RNA A
75. ownload you can disconnect and reconnect your account This will reset your connection to the server Future editions of Geneious will not have this restriction 76 CHAPTER 4 COLLABORATION PRO ONLY Bibliography 1 SF Altschul W Gish W Miller EW Myers and DJ Lipman Basic local alignment search tool J Mol Biol 215 1990 no 3 403 410 15 20 32 35 67 2 MO Dayhoff ed Atlas of protein sequence and structure vol 5 National biomedical re search foundation Washington DC 1978 59 60 3 R Durbin S Eddy A Krogh and G Mitchison Biological sequence analysis Cambridge University Press 1998 61 4 J Felsenstein Confidence limits on phylogenies An approach using the bootstrap Evolution 39 1985 no 4 783 791 65 5 DF Feng and RF Doolittle Progressive sequence alignment as a prerequisite to correct phyloge netic trees J Mol Evol 25 1987 no 4 351 60 61 6 O Gotoh An improved algorithm for matching biological sequences J Mol Biol 162 1982 705 708 59 7 M Vingron HA Schmidt K Strimmer and A von Haeseler Tree puzzle maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 18 2002 no 3 502 504 16 8 M Hasegawa H Kishino and T Yano Dating of the human ape splitting by a molecular clock of mitochondrial dna J Mol Evol 22 1985 no 2 160 174 65 9 S Henikoff and JG Henikoff Amino acid substitution matrice
76. peat regions caused by duplica tion e A random scattering of dots reflects a lack of significant similarity These dots are caused by short sub sequences that match by chance alone For more information on dotplots refer to the paper by Maizel amp Lenk 13 3 5 Pairwise sequence alignments A pairwise sequence alignment is an attempt to determine the regions of homology in two se quences Over evolutionary time related DNA sequences diverge through the accumulation of nucleotide substitutions insertions and deletions As a result an alignment is essential to eval uate the degree of similarity between two related sequences If two nucleotides or amino acids are present in the same column of a pairwise sequence alignment they are aligned This im plies that they are homologous and have evolved from a common ancestral nucleotide amino acid While the aligned nucleotides indicate common ancestry the regions of a pairwise alignment that contain gaps represent areas where insertions or deletions have occurred in the evolution ary history of one or both of the sequences Pairwise alignments can be of two main types local and global A Local Alignment A local alignment is an alignment of two sub regions of a pair of sequences 19 This type of alignment is appropriate when aligning two segments of genomic DNA that may have local regions of similarity embedded in a background of a non homologous sequence A Global Alignment
77. ples 2 tes measures and the NUMI Roald Forsberg Alexei J Drummond Jotun Hein 2004 BMC Genet 6 35 k Molecular phylogeny of coleoid cephalopods Mollusca Cephalopoda using a multigene approach 4 effect of data partitioning on resolving phylogenies in a Bayesian framework gt x rman e lt Q Molecular phylogeny of coleoi Figure 2 4 Advanced Search 26 CHAPTER 2 DATA HANDLING 2 3 4 Autocompletion of search words Geneious remembers previously searched keywords and offers an auto complete option This works in a similar way to Google or predictive text on your mobile phone If you click within the search field a drop down box will appear showing previously used options 2 4 Agents Geneious offers a simple way for you to continuously receive the latest information on genomes sequences and protein structures This feature is called an agent Each agent is a user defined automated search You can instruct an agent to search any Geneious accessible database at reg ular intervals eg weekly including your contacts on Collaboration This simple but powerful feature ensures that you never miss that critical article or DNA sequence To manage agents click on the agent icon in the toolbar An agent has to be set up before it can be used 2 4 1 Creating agents To set up an Agent click the Agents icon and the create button You now need to specify a set of search criteria in the exact same way as you do for search the
78. port or import your sequences If you do not have ClustalW or are unsure if you do you should attempt to perform a ClustalW alignment without specifying a location and Geneious will present you with options including details on how to download ClustalW and an automatic search for finding its location on your hard drive To perform an alignment using ClustalW select the sequences or alignment you wish to align and select the Alignment button from the Toolbar At the top of the alignment options win dow there are buttons allowing you to select the type of alignment you wish to do Choose ClustalW here and the options available for a ClustalW alignment will be displayed 3 8 BUILDING PHYLOGENETIC TREES 63 The options are e ClustalW Location This should be set to the location of the ClustalW program on your computer Enter the path to it in the text field or click the Browse button to browse for the location If the location is invalid and you attempt to perform an alignment Geneious will tell you and offer the options detailed above for getting or finding ClustalW e Cost Matrix Use this to select the desired cost matrix for the alignment The available options here will change according to the type of the sequences you wish to align You can also click the Custom File button to use a cost matrix that you have on your computer the format of these is the same as for the program BLAST e Gap open cost and Gap extend
79. porter Open reading frame plugin PDF importer PHYLIP exporter PileUp importer RSF importer Sequence Alignment Sequence Concatenation Text Viewer Tree builder Description Provides importing and exporting support for a variety of 3 D structure fil Imports Chromatogram documents Provides Clustal W import Builds alignments using ClustalW Allows you to share your documents with other geneious users and to acce Provides DNA Strider import A viewer which displays the entire source xml for documents This is not i Provides a graphical view of a pair of sequences Provides access to EMBL s database at http www ebi ac uk embl Provides import and export functions for Endnote libraries Provides FASTA file importing exporting facilities Generates a single sequence representing the most common residues at e Provides a graphical view of sequence documents Provides a graphical view of a tree s document A plugin for viewing 3D proteins structures Select a 3D structure documen Provides MEGA export Provides access to NCBI s database at http www ncbi nih gov New sequence documents can be made by pasting or typing residues Provides Newick importing facilities Provides Nexus importing exporting facilities ORF analysis tools Imports PDF documents Provides Phylip export Provides PileUp import Provides RSF import Provides pairwise and multiple sequence alignment algorithms Provides the ability to conc
80. residues within a single sequence Quadruple clicking selects a block of residues in multiple sequences After editing is complete click Save to permanently save the new contents The Pop up menu in the sequence viewer The toolbar actions are available via a pop up menu as well Right click Ctrl click on Mac OS X on any sequence partly highlighted sequence or annotation to show the various options The pop up menu contains the Copy residues action keyboard Ctrl C to copy the selected residues to the system clipboard Printing a sequence view To print a sequence view go to File Print and click OK The view is printed without the options panel It is recommended to turn on Wrap sequence and deselect Colors before printing Wrapping prints the sequence as seen in the sequence viewer and the font size is chosen to fill the horizontal width of the page 44 CHAPTER 2 DATA HANDLING 2 7 2 Dotplot viewer This is a special viewer that appears when two sequences are chosen A dotplot compares two sequences to find regions of similarity Each axis X and Y on the plot represents one of the sequences being compared Figure 2 13 For more information about interpreting dot plots refer to the section on them in chapter 3 EDotplot View Sequence View Chicken 1737 nt Y Zoom Level a Pa 190 2 N y Preferences Stringency 18 Window size 21 a gt a
81. rez Nucleotide database This database in GenBank contains 3 separate components that are also searchable databases EST GSS and CoreNucleotide The core nucleotide database brings together information from three other databases GenBank EMBI and DDBJ These are 20 CHAPTER 2 DATA HANDLING part of the International collaboration of Sequence Databases This database also contains Ref Seq records which are NCBI curated non redundant sets of sequences The Entrez Popset database This database contains sets of aligned sequences that are the result of population phylogenetic or mutation studies These alignments usually describe evolution and population variation The PopSet database contains both nucleotide and protein sequence data and can be used to analyze the evolutionary relatedness of a population The Entrez Protein database This database contains sequence data from the translated coding regions from DNA sequences in GenBank EMBL and DDBJ as well as protein sequences sub mitted to the Protein Information Resource PIR SWISS PROT Protein Research Foundation PRF and Protein Data Bank PDB sequences from solved structures The Entrez Structure database This is NCBI s structure database and is also called MMDB Molecular Modeling Database It contains three dimensional biomolecular experimentally or programmatically determined structures obtained from the Protein Data Bank The PubMed database This is a
82. right hand side of the Toolbar Only matching documents will be shown Ordering columns The fields and values of an added Note Type will appear as columns in the 3 1 DATA FILTERING 55 Document Table These new columns can be used to order the table Take the example of pro tein size A click on the column heading will order the documents in increasing or decreasing order according to their protein size Clicking the column heading again arranges the docu ments in the opposite order An arrow next to the heading indicates if it is in increasing A or decreasing V order Viewing Notes Notes are added into columns defined by their Types and Fields Notes are also shown as an extra tab in the Document Viewer Panel Click on the Notes tab to view your notes Notes can be edited or deleted from here too 3 4 Sequence View Text View Source XML Notes Source xs Source Hame NCBI Protein Date Acquired 01 Aug 2006 Modified from original false Figure 3 4 Viewing Notes Editing and Deleting Notes and Note Types Notes can be edited or deleted from the Documents Viewer Panel and from the Add Note screen Click on the Edit Note Type or Delete Note Type button 3 5 3 1 2 Filtering The Filter is a special feature offered by Geneious It is in the top right hand corner of the Main Toolbar and is used to filter documents based on any information listed in the Documents Table Type in the te
83. s does not restrict you to certain note types You can create new note types to annotate your documents To create a new note type select a document and open the Add Note dialog Click on the Create Note Type button in the left hand panel of this window This brings up a window similar to that displayed in 3 1 Note The Note Type Name and Note Type Description fields distinguish your Note type from other user defined note types They do not have any constraints Here are some examples of Note Types Name Description Data type Protein size Size of the protein in kDa Protein sequences Tree building method Method used to build tree UPGMA Neighbor joining Phylogenetic trees 7 Create New Note Type xj Note Type Name Note Type Description Field Name Field Type Constraints Text y Edit Constraints dp Text coca Figure 3 2 Creating new Note Types You need to decide what other characteristics your Note Type will have Field name This defines what the field will be called It will be displayed alongside columns such as Description and Creation Date in the Documents Table You can have more than one Field in a single Note Type Field type This describes the kind of information that the column contains such as Text Integer and True False The full list of choices in Geneious is shown in 3 2 Constraints These are limiting factors on the data and are specific to e
84. s from protein blocks Proc Natl Acad Sci US A 89 1992 no 22 10915 10919 59 60 10 T Jukes and C Cantor Evolution of protein molecules pp 21 32 Academic Press New York 1969 65 11 S Kumar K Tamura and M Nei Mega3 Integrated software for molecular evolutionary ge netics analysis and sequence alignment Brief Bioinform 5 2004 no 2 150 163 18 12 DR Maddison DL Swofford and WP Maddison Nexus an extensible file format for sys tematic information Syst Biol 46 1997 no 4 590 621 16 18 64 77 78 BIBLIOGRAPHY 13 JV Maizel and RP Lenk Enhanced graphic matrix analysis of nucleic acid and protein se quences Proc Natl Acad Sci US A 78 1981 no 12 7665 9 57 58 14 C Michener and R Sokal A quantitative approach to a problem in classification Evolution 11 1957 130 162 63 64 66 15 SB Needleman and CD Wunsch A general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 48 1970 no 3 443 53 58 59 16 C Notredame DG Higgins and J Heringa T coffee A novel method for fast and accurate multiple sequence alignment J Mol Biol 302 2000 no 1 205 217 15 17 F Ronquist and JP Huelsenbeck Mrbayes 3 Bayesian phylogenetic inference under mixed models Bioinformatics 19 2003 no 12 1572 4 63 18 N Saitou and M Nei The neighbor joining method a new method for reconstructing phyloge netic trees
85. s you search using multiple criteria By clicking the button on right of the search term you can add another search criteria You can remove search criteria by 2 3 SEARCHING DATABASES AND LOCAL DOCUMENTS USING GENEIOUS 25 Match all 43 of the following Document type A is 3 3D structure 3 _ M Include Subfolders Fewer Options 3 Name Summary R Alpha Helix Alpha Helix d Cyclopropane Cyclopropane af VirusVIRAL PROTEIN VirusVIRAL PROTEIN 1G5G AAA Ja AS Figure 2 3 Document type search options clicking on the appropriate button The Match all any of the following option at the top of the search terms determines how these criteria are combined Match Any requires a match of one or more of your search criteria This is a broad search and results in more matches Match All requires a match all of your search criteria This is a narrow search and results in fewer matches Match all 3 of the following Author 3 contains 3 Drummond AJ Date published 3 is between 3 OlJan2003 and 31 Dec 2005 Create Agent Fewer Options Name Summary Z A Choosing appropriate substitution models for the phylogenetic analysis of protein coding seque Choosing appropriate substitu b Shapiro Andrew Rambaut amp Alexei J Drummond 2005 Mol Biol Evol 23 7 9 Qa Tree measures and the number of segregating sites in time structured population sam
86. sources e Organize your data into easily accessible folders e Automatically update your data Know the purpose of each panel in Geneious Customize Geneious to meet your needs 2 1 Importing and exporting data Geneious is able to import raw data from different applications and export the results in a range of formats If you are new to bioinformatics please take the time to familiarize yourself with this chapter as there are a number of formats to be aware of 2 1 1 Importing data from the hard drive to your Local folders To import files from your hard disk click File Import From file This will open up a file dialog Select one or more files and click Import If Geneious automatic file format detection fails select the file type you wish to import Figure 2 1 before selecting the name of the file s The different file types are described in detail in the next section 13 14 CHAPTER 2 DATA HANDLING File name Files of type Geneious geneious Endnote 8 0 xml A Nexus nex PDF pdf 3 D structure documents pdb mol xyz cml gpr hin nwo Fasta Nucleotide fasta Fasta Protein Fasta Unformatted sequence seq Newick newick tree Figure 2 1 File import options 2 1 2 Data input formats Geneious version 2 0 can handle all the following file formats Format Extensions Data types Common sources Clust
87. tide F PopSet Protein 2 PubMed Structure soo Taxonomy A erv alignment DO EUMERt TABE ABZ34101 1 AB Sequence View Text View 4B234107 1 4B234104 1 AB234103 1 Similarity AB234101 1 Cursor before residue 85 ungapped residue 85 E tract E Reverse Complement E slate A Y Annotation mi ave ja Document Viewer Panel cres GHACHACG ESGHACCCHE CHAAAAGHGN MET 50 60 You can drag and drop articles and sequences that you find in external databases for example NCBI into this folder for future reference our Help Panel Right click on this folder and select Share Folder to allow your contacts to search it over the Collaboration service If you share a folder its sub folders are always also shared Any folders you share can be searched by all your contacts Figure 2 8 Geneious main window 34 CHAPTER 2 DATA HANDLING This information is presented in table form Figure 2 9 Name Summary ldentical Journal Title First Author PMID Sequence Resi URLFR A e a at la aa Science Roman Biek 16439664 http ww history of its carnivore host Aa Population genetic estimation Population genetic estacion of the loss of genetic diversity a BMC Evol Biol Charles T T 16556318 http ww during horizontal transmission of HIV 1 Relaxed phylogenetics and dating with confidence 2 Relaxed phylogenetics and da Al
88. trl C Command C Select the destination folder and Paste Ctrl V Command V the document into it 2 5 2 Searching your Local folders The Services Panel allows you to browse your Local folder hierarchy Next to each folder name in the hierarchy is the number of documents it contains in brackets When the Local folder or a sub folder is collapsed minimized the brackets next to the folder shows how many files are contained in that folder as well as all of its sub folders In addition if some of the documents in a folder are unread the number of unread documents will also appear in the brackets You can search the Local folder and sub folders the same way you search the public databases by clicking on the Search icon If you have defined a new type of note in Geneious and a Note has been added it will also be added to the Advanced Search criteria Look at an example of a new Note type called Protein size which takes a text value for the protein in kDa kiloDaltons see Figure 2 6 2 5 STORING DATA IN GENEIOUS 31 Match all E of the following Any Field a contains E Document type geneious document type E Value First Author The article principal author tluc GID The Height T ank ID of the sequence E eight on of hit in result sequence Journal Title Where article v Last Author The article Medline Date The arti tion date Molecule Type The molecule type of the sequence Nam
89. unt The process is the same in each case Select an online account or an online contact You will see a search panel just as you would for an online database If you search an account you will retrieve documents from all contacts who are online If you search just a contact you will retrieve documents from that contact alone You can also set up agents just as you would for any database The agents will fail if they try to search when an account of a contact is offline though 4 4 SEARCHING CONTACTS 75 NOTE The search panel is still enabled and you can still click the Search button if a contact is offline This is so that documents you have downloaded are still available if a contact suddenly goes offline Any attempt to search that contact will fail of course 4 4 1 Concurrency The current iteration of Collaboration is somewhat restricted in that it can only send one mes sage to the server at a time This means that if you search several contacts at once you are really searching them one after the other Additionally when someone downloads a document from you it is actually your copy of Geneious sending a message to theirs and it must complete this before it attempts the next search If someone is downloading a large document from you you will see the text busy next to your account name Searches will not complete while your account is busy If you really need to do a search and you don t mind interrupting someone else s d
90. ve an options panel occupying the right of the document viewer The options in the options panel have an arrow which can be used to expand or hide a group of related options See the next section on document viewers for more information about operating the various viewers in Geneious 2 6 4 The Help Panel The Help Panel has a Help tab and a Tutorial tab The Help tab provides you information about the service you are currently using The Tutorial is aimed at first time users of Geneious and has been included to provide a feel for how Geneious works It is highly recommended 36 CHAPTER 2 DATA HANDLING that you work through the tutorial if you haven t used Geneious before 2 6 5 The Toolbar The toolbar contains several icons that provide shortcuts to common functions in Geneious You can alter the contents of the toolbar to suit your own needs The icons can be displayed small or large and with or without their labels The Preferences and Help icons are always available The Back and Forward options help you move between previous views in Geneious and are analogous to the back and forward buttons in a web browser The V op tion shows a list of previous views The other features that can be accessed form the toolbar are described in chapter 3 The toolbar can be customized by right clicking Ctrl Click on MacOS on it This gives a popup menu with the following options e Show Labels Turn the text labels o
91. vices Panel and choose Add Contact from the menu at the top or right click on your account in the Services Panel and choose the same option You will see a simple dialog with one field Jabber ID A Jabber ID looks like an email address and has a similar function It uniquely identifies some other Geneious users account You can enter a contact s Jabber ID directly into this field if you know it To see your own Jabber ID hover your mouse over your account in the Services Panel and it will appear in a tool tip If the server supports it you should also see a Search For Contact link Click this to go to the next dialog 4 2 MANAGING YOUR CONTACTS 73 7 Add Contact to MyAccount x Jabber ID e g user name talk geneious com Y Search For Contact Done Figure 4 3 Add Contact dialog box Here you will see a box for a search string and some checkboxes indicating what you are searching on Enter all or part of the name or email of the contact you want and click the Search button If any rows are returned in the results table you will be able to select one or entries and add them as contacts 7 Add Contact to MyAccount 3 xj Search V Username V Name V Email Add Gontact lt Enter Contact ID Figure 4 4 Add New Contact dialog box in searching mode Your new contact will appear immediately in your contact list however you will not be able to tell whether your new contact is online until they accept you as
92. wick format and display them in the visualization win dow It also gives you a number of display options including tree types branch lengths and labels Nexus format The Nexus format 12 was designed to standardize the exchange of phylogenetic data in cluding sequences trees distance matrices and so on The format is composed of a number of blocks such as TAXA TREES and CHARACTERS Each block contains pre defined fields Geneious imports and exports files in Nexus format and can process the information stored in them for analysis PileUp format The PileUp format is used by the pileup program a part of the Genetics Computer Group GCG Wisconsin Package Rich Sequence format RSF Rich Sequence Format files contain one or more sequences that may or may not be related In addition to the sequence data each sequence can be annotated with descriptive sequence 2 1 IMPORTING AND EXPORTING DATA 17 information DNA Strider Sequence files generated by the Mac program DNA Strider containing one Nucleotide or Pro tein sequence PDB format Protein Databank files contain a list of XYZ co ordinates that describe the position of atoms in a protein These are then used to generate a 3D model which is usually viewed with Rasmol or SPDB viewer Geneious can read PDB format files and display an interactive 3D view of the protein structure including support for displaying the protein s secondary structure when the appropriate inf
93. ws you to directly download information from seven important NCBI databases NCBI 2 2 ACQUIRING DATA FROM PUBLIC DATABASES 19 BLAST services and one EMBL database Table 2 1 Table 2 1 NCBI and EMBL databases accessible via Geneious Database Center Coverage Genome NCBI Whole genome sequences Nucleotide NCBI DNA sequences PopSet NCBI sets of DNA sequences from population studies Protein NCBI Protein sequences Structure NCBI 3D structural data PubMed NCBI Biomedical literature citations and abstracts Taxonomy NCBI Names and taxonomy of organisms Uniprot EMBL Protein sequences This section gives a brief explanation of the key databases that can be searched using Geneious There is also a bewildering array of acronyms If you are not already a bioinformatician please check them before you continue Table 2 2 Acronyms Acronym Full name DDBJ DNA Data Bank of Japan EMBL European Molecular Biology Laboratory cDNA Complementary DNA GSS Genomic survey sequences PDB Protein Data Bank Bol Expressed Sequence Tags UniProt the Universal Protein Resource RefSeq Reference Sequence PIR Protein Information Resource PRF Protein Research Foundation STS Sequence Tagged Site HTGS High Throughput Genomic Sequence The Entrez Genome database This provides views of a variety of genomes complete chromo somes Sequence maps with contigs contiguous sequences and integrated genetic and physi cal maps The Ent
94. xt you are searching for and Geneious will display all the documents that match this text and hide all other documents in the Document Table To view all the documents in a folder clear the Filter box of text or click the button 56 CHAPTER 3 DATA PROCESSING Existing Note Types Note Person gt Create Note Type Delete Note Type A Edit Note Type Figure 3 5 Viewing Notes Filtering on the fly Filtering can be used while searching for documents via public databases filtering data as it is being downloaded Type in the appropriate text in the Filter Box and only those documents that match both the original criteria as specified by the search terms and the Filter text will be displayed This is an effective way of filtering within your search results 3 2 Literature Geneious allows you to search for relevant literature in NCBI s PubMed database The results of this search are summarized in columns in the Document Table and include the PubMed ID PMID first and last authors URL if available and the name of the Journal When a document is selected the abstract of the article is displayed in the Document Viewer along with a link to the full text of the document if available and a link to Google Scholar both below the author s name s Note If the full text of the article is available for download in PDF format it can also be stored in Geneious by saving it to your hard drive and then importing it This wi
95. ys the pl of the protein at every position along the sequence or the average pI when multiple sequences are being viewed Sliding window size This calculates the value of the graph at each position by averaging across a number of surrounding positions When the value is 1 no averaging is performed When the 40 CHAPTER 2 DATA HANDLING value is 3 the value of the graph is the average of the residue value at that position and the values on either side Chromatogram This is available with chromatogram traces It displays the four traces above the sequence where the peak as detected by the base calling program is at the middle of the base letter When viewing more than one chromatogram or an alignment made from chro matograms each chromatogram can be turned on or off individually using the checkbox s below Note that since the distance between bases as inferred from the trace varies the trace may be either contracted or expanded compared with the raw data Show quality This is available with enabled chromatogram traces It displays a quality measure typically Phred quality scores for each base as assessed by the base calling program The quality is shown as a shaded bar graph overlaid on top of the chromatogram Note that those scores represent an estimate of error probability and are on a logarithmic scale the highest bar represents a one in a million 10 probability of calling error while the middle represents a probability of only

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