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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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<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
-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
- click the "Fetch DAS Features" button.
- <ul>
- <li>Cancelling Feature Retrieval<br>
- Press the <strong>Cancel Fetch</strong> button to immediately stop
- feature retrieval. This will not remove any features already added to
- the alignment, but will halt any outstanding DAS requests.<em>The
- cancel fetch button is of particular use when one or more DAS
- annotation servers are not responding!</em>
- </ul>
- </li>
-</ol>
-<p>If your DAS source selection contains sources which use Uniprot
-accession ids, you will be asked whether Jalview should find Uniprot
-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.
-<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
- retrieval process.</li>
-</ul>
-<p>
-<p><em>DAS support was introduced in Jalview Version 2.1.</em></p>
-<p>
+ <p>
+ <strong>DAS Sequence Feature Retrieval</strong>
+ </p>
+ <p>Jalview includes a client for retrieving sequences and their
+ features via the Distributed Annotation System.</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 retrieval, then
+ click the "Fetch DAS Features" button.
+ <ul>
+ <li>Cancelling Feature Retrieval<br> Press the <strong>Cancel
+ Fetch</strong> button to immediately stop feature retrieval. This
+ will not remove any features already added to the alignment,
+ but will halt any outstanding DAS requests.<em>The cancel
+ fetch button is of particular use when one or more DAS
+ annotation servers are not responding!</em>
+ </ul>
+ </li>
+ </ol>
+ <p>
+ If your DAS source selection contains sources which use UniProt
+ accession ids, you will be asked whether Jalview should find UniProt
+ 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> 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 ID retrieval process.</li>
+ </ul>
+ <p>
+ <p>
+ <em>DAS support was introduced in Jalview Version 2.1.</em>
+ </p>
+ <br />
+ <p>
+ <em>The DAS registry at http://www.dasregistry.org was
+ decommissioned early in 2015. An unmaintained mirror is currently
+ hosted at http://www.ebi.ac.uk/das-srv/registry/.</em>
+ </p>
+ <p>
</body>
</html>
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