3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Sequence Fetcher</title>
23 <p><strong>Sequence Fetcher</strong></p>
24 <p>Jalview can retrieve sequences from certain databases using
25 either the WSDBFetch service provided by the European Bioinformatics
26 Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em>
27 command (configured in <a href="dassettings.html">DAS settings</a>).</p>
28 <img src="seqfetcher.gif" align="center"
29 alt="The Jalview Sequence Fetcher Dialog Box">
30 <p>The Sequence Fetcher dialog box can be opened via the
31 "File" menu on the main desktop in order to retrieve sequences
32 as a new alignment, or opened via the "File" menu of an
33 existing alignment to import additional sequences. Please note, there
34 will be a short delay when the sequence fetcher is first opened, whilst
35 Jalview compiles the list of available sequence datasources from the
36 currently defined DAS server registry.</strong></p>
37 <p>First, select the database you want to retrieve sequences from.
38 Then, enter one or more accession ids (as a semi-colon separated list),
39 or press the "Example" button to paste the example accession
40 for the currently selected database into the retrieval box. Finally,
41 press "OK" to initiate the retrieval.</p>
42 <p><em>Fetching Individual PDB Chains</em><br>
43 If you are retrieving sequences from the PDB, you can retrieve specific
44 chains by appending a colon and the chain id to the PDB id. For example
48 <p><em>Retrieving parts of large sequence records</em><br>
49 When retrieving from DAS sequence sources, coordinate range arguments
50 can be passed to the server using the standard DAS sequence command
52 <AccessionId>:<start>,<end></pre> If you know a source
53 understands this type of query format, then you should untick the
54 checkbox for 'replace commas with semi-colons' so the range query can be
55 passed to the server; otherwise, the query will be split into two (e.g
56 'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases,
57 however, a source that supports range queries will include a range
58 qualification in its example query, and Jalview will then automatically
59 disable the 'replace commas with semi-colons' option.<br>
60 <em>The option to disable the comma to semi-colon translation was
61 added in Jalview 2.6</em></p>
62 <p>If you use the WSDBFetch sequence fetcher services (EMBL,
63 Uniprot, PDB and PFAM) in work for publication, please cite:</p>
64 <p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S.,
65 Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
67 SOAP-based services provided by the European Bioinformatics Institute.<br>
68 Nucleic Acids Res. 33(1):W25-W28 (2005) <br>