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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
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-<head><title>Sequence Fetcher</title></head>
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Sequence Fetcher</title>
+</head>
<body>
<p><strong>Sequence Fetcher</strong></p>
<p>Jalview can retrieve sequences from certain databases using either the
-WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
-<img src="seqfetcher.gif" align="center" alt="The Jalview Sequence Fetcher Dialog Box">
-<p>The Sequence Fetcher dialog box can be opened via the "File"
+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>
+ <img src="seqfetcher.gif" align="center"
+ alt="The Jalview Sequence Fetcher Dialog Box">
+ <p>The Sequence Fetcher dialog box can be opened via the "File"
menu on the main desktop in order to retrieve sequences as a new
alignment, or opened via the "File" menu of an existing alignment
- to import additional sequences. Please note, there will be a short delay when the sequence fetcher is first opened,
+ to import additional sequences. There may be a short delay when the sequence fetcher is first opened,
whilst Jalview compiles the list of available sequence datasources from the
- currently defined DAS server registry.</strong>
+ currently defined DAS server registry.
</p>
-<p>First, select the database you want to retrieve sequences from. Then, enter
+ <p>First, select the database you want to retrieve sequences from
+ by clicking the button labeled 'Select database retrieval source'. If
+ a database source is already selected, then the button's label will
+ change to show the currently selected database.</p>
+ <img src="selectfetchdb.gif" align="left" alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+ <p>Since Jalview 2.8, the
+ available databases are shown as a tree in a popup dialog box. The
+ databases are ordered alphabetically, and if there are many sources
+ for the same type of sequence identifier, they will be grouped
+ together in a sub-branch branch labeled with the identifier.</p>
+ <p>Once you have selected the sequence database using the popup dialog box, enter
one or more accession ids (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the currently selected database into the retrieval box.
Finally, press "OK" to initiate the retrieval.</p>
-<p>
+ <p><strong>Specifying chains for PDB IDs</strong>
If you are retrieving sequences from the PDB, you can retrieve
specific chains by appending a colon and the chain id to the PDB
- id. For example :<br><pre> 1GAQ:A</pre><br>When retrieving from DAS sequence sources,
- coordinate range arguments can be passed to the server using the standard DAS
- sequence command format (<strong>:<start>,<end></strong>)</p>
-<p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB and PFAM)
+ id. For example :<br/><pre> 1GAQ:A</pre>
+ </p>
+ <p>
+ <strong>Only retrieving part of a sequence</strong> DAS sources
+ (indicated by a "<em>(DAS)</em>") allow a range to be
+ specified in addition to a sequence ID. To retrieve 50 residues
+ starting at position 35 in UNIPROT sequence P73137 using the UNIPROT
+ DAS server, you would enter "'P73137:35,84'.<br/><em>Full support for DAS range queries was introduced in Jalview 2.8</em>
+ </p>
+
+<p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM)
in work for publication, please cite:</p>
<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>
git://source.jalview.org / jalview.git / blobdiff