<html>
-
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<head>
<title>DAS Features</title>
</head>
<body>
<p><strong>DAS Sequence Feature Retrieval</strong></p>
-<p>Jalview includes a client for retrieving sequence features via
+<p>Jalview includes a client for retrieving sequences and their features via
the <a href="http://www.biodas.org">Distributed Annotation System</a>.</p>
<ol>
<li>Open the Feature Settings panel by selecting "View ->
Feature Settings..."</li>
<li>Click on the "<a href="dassettings.html">DAS Settings</a>"
tabbed pane.</li>
- <li>Select the sources to use for DAS feature retireval, then
+ <li>Select the sources to use for DAS feature retrieval, then
click the "Fetch DAS Features" button.
<ul>
<li>Cancelling Feature Retrieval<br>
Accession ids for the given sequence names. It is important to realise
that many DAS sources only use Uniprot accession ids, rather than
Swissprot/Uniprot sequence names.<br>
-<p><strong>The Sequence Identification Process</strong></p>
-The method of Uniprot accession id discovery is the same method which
-earlier Jalview versions used for sequence feature retrieval, and is now
-also used for
-<a href="viewingpdbs.html">PDB ID discovery</a>
-. Essentially, Jalview will try to retrieve Uniprot records via the
-EBI's WSDbFetch interface using each sequence's ID string (or each
-string in the ID separated by the '∣' symbol).
-</p>
-<p>If a uniprot record (or set of records) is found for a sequence,
-then the sequence is aligned to the one in the Uniprot record to
-determine the correct start and end residue positions (which are
-displayed when the 'Show Full Sequence ID' option is set).</p>
-<p>If the alignment reveals differences between the sequence in the
-alignment and the one in the record, then Jalview will assume that the
-aligned sequence is not the one in the uniprot record.</p>
-<p>In some cases, the ID used to retrieve Uniprot records may be out
-of date and a dialog box will be opened indicating that a 100% match
-between the sequence and a Uniprot record was identified, but the
-sequence name is different. In this case, the ID must be manually
-changed (by right clicking on the sequence ID and selecting <strong>Sequence→Edit
-Name</strong>), before Jalview will show its sequence features.
+The <a href="../webservices/dbreffetcher.html">database reference
+fetcher</a> documentation describes how Jalview discovers what database
+references are appropriate for the sequences in the alignment.
<ul>
<li><em>Note</em><br>
Please remember to save your alignment if either the start/end
- numbering, or the sequence IDs were updated during the Uniprot ID
+ numbering, or the sequence IDs were updated during the ID
retrieval process.</li>
</ul>
<p>
git://source.jalview.org / jalview.git / blobdiff