-<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>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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>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" 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><em>Fetching Individual PDB Chains</em><br>
+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>
+</p>
+<p><em>Retrieving parts of large sequence records</em><br>
+When retrieving from DAS sequence sources, coordinate range arguments
+can be passed to the server using the standard DAS sequence command
+format:<pre>
+ <AccessionId>:<start>,<end></pre> If you know a source
+understands this type of query format, then you should untick the
+checkbox for 'replace commas with semi-colons' so the range query can be
+passed to the server; otherwise, the query will be split into two (e.g
+'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases,
+however, a source that supports range queries will include a range
+qualification in its example query, and Jalview will then automatically
+disable the 'replace commas with semi-colons' option.<br>
+<em>The option to disable the comma to semi-colon translation was
+added in Jalview 2.6</em></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 / blobdiff