--- /dev/null
+<html>\r
+\r
+<head><title>DAS Features</title></head>\r
+\r
+<body>\r
+<p><strong>DAS Sequence Feature Retrieval</strong></p>\r
+<p>Jalview 2.1 can be set up to retrieve sequence features using the <a href="http://www.biodas.org">Distributed \r
+ Annotation System</a></p>\r
+<ol>\r
+ <li>Open the Feature Settings panel by selecting "View -> Feature Settings..."</li>\r
+ <li>Click on the "<a href="dassettings.html">DAS Settings</a>" tabbed \r
+ pane.</li>\r
+ <li>Select the sources to use for DAS feature retireval, then click the "Fetch \r
+ DAS Features" button.</li>\r
+</ol>\r
+<p>If your DAS source selection contains sources which use Uniprot accession ids, \r
+ you will be asked whether Jalview should find Uniprot Accession ids for the \r
+ given sequence names. It is important to realise that many DAS sources only \r
+ use Uniprot accession ids, not names of sequences. <br>\r
+ The method of Uniprot accession id discovery is the same method which earlier \r
+ Jalview versions used for sequence feature retrieval, ie WSDbFetch provided \r
+ by the EBI.</p>\r
+<p>The process is as described:</p>\r
+<p><strong>The Sequence Identification Process</strong> </p>\r
+<p>Jalview will attempt to retrieve sequence features from Uniprot files using \r
+ the EBI dbFetch web service using the given sequence names (or Uniprot ID, if \r
+ available). A 100% match with the Uniprot record is required for Uniprot features \r
+ to be view on a sequence.</p>\r
+<p>The first step in the procedure for matching uniprot IDs to sequences is to \r
+ use the ID (name) of each sequence to retrieve Uniprot records directly.</p>\r
+<p> If a uniprot record (or set of records) is found for a sequence, then the \r
+ sequence is aligned to the one in the Uniprot record to determine the correct \r
+ start and end residue positions (which are displayed when the 'Show Full Sequence \r
+ ID' option is set). </p>\r
+<p>If the alignment reveals differences between the sequence in the alignment \r
+ and the one in the record, then Jalview will assume that the aligned sequence \r
+ is not the one in the uniprot record. </p>\r
+<p> In some cases, the ID used to retrieve Uniprot records may be out of date \r
+ and you will be notified of that a 100% match between the sequence and a Uniprot \r
+ record was identified, but the sequence name must be manually changed (by right \r
+ clicking on the sequence ID and selecting <strong>Sequence→Edit Name</strong>), \r
+ before Jalview will show its sequence features. \r
+<ul>\r
+ <li>remember to save your alignment if you have updated any of the sequence \r
+ IDs! </li>\r
+</ul>\r
+<p> \r
+<p>\r
+<p> \r
+</body>\r
+</html>\r
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