-<html>\r
-<head><title>Sequence Fetcher</title></head>\r
-<body>\r
-<p><strong>Sequence Fetcher</strong></p>\r
-<p>Jalview can retrieve sequences from certain databases via the\r
-WSDBFetch service provided by the European Bioinformatics Institute.</p>\r
-<p>A Sequence Fetcher dialog box can be opened via the "File" \r
- menu on the main desktop in order to retrieve sequences as a new\r
- alignment, or opened via the "File" menu of an existing alignment\r
- to import additional sequences.\r
-</p>\r
-<p>Select the database you want to retrieve sequences from, and enter\r
- the database id (or a semi-colon separated list of several ids) in\r
- the text box. Finally, press OK to initiate the retrieval.</p>\r
-<p>\r
- If you are retrieving sequences from the PDB, you can retrieve\r
- specific chains by appending a colon and the chain id to the PDB\r
- id. For example :<br><pre> 1GAQ:A</pre></p>\r
-<p>If you use the sequence fetcher in work for publication, please cite:</p>\r
-<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar \r
- S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>\r
- SOAP-based services provided by the European Bioinformatics Institute.<br>\r
- Nucleic Acids Res. 33(1):W25-W28 (2005) <br>\r
- <br>\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<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 DAS servers capable of the <em>sequence</em> command (<em>since version 2.4</em>).</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,
+ whilst Jalview compiles the list of available sequence datasources from the
+ currently defined DAS server registry.</strong>
+</p>
+<p>First, select the database you want to retrieve sequences from. Then, 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>
+ 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)
+ 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>
+ SOAP-based services provided by the European Bioinformatics Institute.<br>
+ Nucleic Acids Res. 33(1):W25-W28 (2005) <br>
+ <br>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff
