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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
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+ * of the License, or (at your option) any later version.
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* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
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+ * 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 DBFetch service provided by the EMBL European Bioinformatics
+ Institute, or, 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, <strong>select the database you want to retrieve
+ sequences from</strong> 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, <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.
+ </p>
+ <p>
+ <strong>Fetching from The PDB with the EMBL-EBI PDBe Search
+ Interface</strong>
+ </p>
+ <p>
+ Since Jalview 2.9, selecting PDB as the sequence database will open
+ the <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> for
+ discovering and retrieving structures.
+ </p>
+ <p>
+ <strong>Only retrieving part of a sequence</strong>
+ </p>
+ <p>
+ 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, 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>