-<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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 a range of sequence, 3D
+ structure, genomic and domain family databases provided by EMBL-EBI.</p>
+ <p>The Sequence Fetcher 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 contacts each database's web API.</p>
+ <p>
+ Every time a new fetcher is opened, you will need to <strong>select
+ the database you want to retrieve sequences</strong> from the database
+ chooser.
+ </p>
+ <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+ <p>
+ The databases are shown as a tree, and ordered alphabetically;
+ tooltips are shown if you mouse over some sources, explaining what
+ the database will retrieve. You can select one by using the up/down
+ arrow keys and hitting return, or by double clicking with the mouse.
+ </p>
+ <p>Once you have selected a sequence database, its fetcher dialog
+ will open. Jalview provides two types of dialog:</p>
+ <ol>
+ <li><strong>The Free-text Search Interface</strong> <br />Free-text
+ search clients are provided for PDB (Since 2.9), and UniProt
+ (Since 2.10). They provide access to each database's own query
+ system, enabling you to retrieve data by accession, free text
+ description, or any other type of supported field. For full
+ details, see each client's help page:
+ <ul>
+ <li><a href="pdbsequencefetcher.html">PDB Sequence
+ Fetcher</a></li>
+ <li><a href="uniprotsequencefetcher.html">UniProt
+ Sequence Fetcher</a></li>
+ </ul></li>
+ <li><strong>Accession based sequence retrieval</strong> <br />
+
+ <img src="seqfetcher.gif" align="center"
+ alt="The Jalview Sequence Fetcher Dialog Box"><br /> To
+ retrieve sequences, simply <strong>enter one or more
+ accession ids</strong> (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.</li>
+ </ol>
+
+ <p>If you use the WSDBFetch sequence fetcher services (EMBL,
+ UniProt, 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>
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