-<html>\r
-<head><title>Sequence Fetcher</title></head>\r
-<body>\r
-<p><strong>Sequence Fetcher</strong></p>\r
-<p>The Sequence Fetcher can be started from the main desktop "File" \r
- menu or from a particular alignment window.</p>\r
-<p>Select which database to fetch your sequence from and enter the sequence id. \r
- If you are retrieving sequences from PDB database and you know which chain you \r
- would like to retrieve, append the chain id after colon to the PDB id. eg 1GAQ:A</p>\r
-<p>The Sequence Fetcher uses WSDBFetch provided by the European Bioinformatics \r
- Institute. If you use this service please quote:</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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<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. There may 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.
+</p>
+ <p>First, select the database you want to retrieve sequences from
+ by clicking the button labeled 'Select database retrieval source'. If
+ a database source is already selected, then the button's label will
+ change to show the currently selected database.</p>
+ <img src="selectfetchdb.gif" align="left" alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+ <p>Since Jalview 2.8, the
+ available databases are shown as a tree in a popup dialog box. The
+ databases are ordered alphabetically, and if there are many sources
+ for the same type of sequence identifier, they will be grouped
+ together in a sub-branch branch labeled with the identifier.</p>
+ <p>Once you have selected the sequence database using the popup dialog box, 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><strong>Specifying chains for PDB IDs</strong>
+ 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>
+ <strong>Only retrieving part of a sequence</strong> DAS sources
+ (indicated by a "<em>(DAS)</em>") allow a range to be
+ specified in addition to a sequence ID. To retrieve 50 residues
+ starting at position 35 in UNIPROT sequence P73137 using the UNIPROT
+ DAS server, you would enter "'P73137:35,84'.<br/><em>Full support for DAS range queries was introduced in Jalview 2.8</em>
+ </p>
+
+<p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM)
+ 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