3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Sequence Fetcher</title>
27 <strong>Sequence Fetcher</strong>
30 Jalview can retrieve sequences from certain databases using either
31 the DBFetch service provided by the EMBL European Bioinformatics
32 Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em>
33 command (configured in <a href="dassettings.html">DAS settings</a>).
35 <p>The Sequence Fetcher can be opened via the
36 "File" menu on the main desktop in order to retrieve
37 sequences as a new alignment, or opened via the "File"
38 menu of an existing alignment to import additional sequences. There
39 may be a short delay when the sequence fetcher is first opened,
40 whilst Jalview compiles the list of available sequence datasources
41 from the currently defined DAS server registry.</p>
43 Every time a new fetcher is opened, you will need to <strong>select the database you want to retrieve
44 sequences</strong> from the database chooser.
46 <img src="selectfetchdb.gif" align="left" width="480" height="204"
47 alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)"
49 <p>The databases are shown as a tree, and ordered alphabetically;
50 tooltips are shown if you mouse over some sources, explaining what
51 the database will retrieve. You can select one by using the up/down
52 arrow keys and hitting return, or by double clicking with the mouse.
53 <br/><em>If you have DAS sources enabled, then you may have several sources
54 for the same type of sequence identifier, and these will be grouped
55 together in a sub-branch branch labeled with the identifier.</em></p>
56 <p>Once you have selected a sequence database, its fetcher dialog
57 will open. Jalview provides two types of dialog:</p>
58 <ol><li><strong>The Free-text Search Interface</strong>
60 <br/>Free-text search clients are provided for PDB (Since 2.9), and
61 UniProt (Since 2.10). They provide access to each database's own
62 query system, enabling you to retrieve data by accession, free text
63 description, or any other type of supported field. For full details,
64 see each client's help page:
66 <li><a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a></li>
67 <li><a href="uniprotsequencefetcher.html">UniProt Sequence
71 <li><strong>Accession based sequence retrieval</strong>
74 <img src="seqfetcher.gif" align="center"
75 alt="The Jalview Sequence Fetcher Dialog Box"><br/>
76 To retrieve sequences, simply <strong>enter one or more accession ids</strong> (as a semi-colon
77 separated list), or press the "Example" button to paste the
78 example accession for the currently selected database into the
79 retrieval box. Finally, press "OK" to initiate the
84 <strong>Only retrieving part of a sequence</strong>
87 When using DAS sources (indicated by a "<em>(DAS)</em>"),
88 you can append a range in addition to a sequence ID. For example, to
89 retrieve 50 residues starting at position 35 in UNIPROT sequence
90 P73137 using the UNIPROT DAS server, you would enter
91 "'P73137:35,84'.<br /> <em>Full support for DAS range
92 queries was introduced in Jalview 2.8</em>
95 <p>If you use the WSDBFetch sequence fetcher services (EMBL,
96 UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
98 Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
99 J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
100 R. <br> SOAP-based services provided by the European
101 Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28