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23 <title>Sequence Fetcher</title>
26 <p><strong>Sequence Fetcher</strong></p>
27 <p>Jalview can retrieve sequences from certain databases using either the
28 WSDBFetch service provided by the European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
29 <img src="seqfetcher.gif" align="center"
30 alt="The Jalview Sequence Fetcher Dialog Box">
31 <p>The Sequence Fetcher dialog box can be opened via the "File"
32 menu on the main desktop in order to retrieve sequences as a new
33 alignment, or opened via the "File" menu of an existing alignment
34 to import additional sequences. There may be a short delay when the sequence fetcher is first opened,
35 whilst Jalview compiles the list of available sequence datasources from the
36 currently defined DAS server registry.
38 <p>First, select the database you want to retrieve sequences from
39 by clicking the button labeled 'Select database retrieval source'. If
40 a database source is already selected, then the button's label will
41 change to show the currently selected database.</p>
42 <img src="selectfetchdb.gif" align="left" alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
43 <p>Since Jalview 2.8, the
44 available databases are shown as a tree in a popup dialog box. The
45 databases are ordered alphabetically, and if there are many sources
46 for the same type of sequence identifier, they will be grouped
47 together in a sub-branch branch labeled with the identifier.</p>
48 <p>Once you have selected the sequence database using the popup dialog box, enter
49 one or more accession ids (as a semi-colon separated list), or press the
50 "Example" button to paste the example accession for the currently selected database into the retrieval box.
51 Finally, press "OK" to initiate the retrieval.</p>
52 <p><strong>Specifying chains for PDB IDs</strong>
53 If you are retrieving sequences from the PDB, you can retrieve
54 specific chains by appending a colon and the chain id to the PDB
55 id. For example :<br/><pre> 1GAQ:A</pre>
58 <strong>Only retrieving part of a sequence</strong> DAS sources
59 (indicated by a "<em>(DAS)</em>") allow a range to be
60 specified in addition to a sequence ID. To retrieve 50 residues
61 starting at position 35 in UNIPROT sequence P73137 using the UNIPROT
62 DAS server, you would enter "'P73137:35,84'.<br/><em>Full support for DAS range queries was introduced in Jalview 2.8</em>
65 <p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM)
66 in work for publication, please cite:</p>
67 <p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
68 S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>
69 SOAP-based services provided by the European Bioinformatics Institute.<br>
70 Nucleic Acids Res. 33(1):W25-W28 (2005) <br>