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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
*
* 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.
- *
+ * 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/>.
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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>Web Service Menu</title>
+</head>
+
+<body>
+ <p>
+ <strong>Web Service Menu</strong><br /> <em>This menu is
+ dynamic, and may contain user-defined web service entries in
+ addition to any of the following ones:</em>
+ <ul>
+ <li><strong>Fetch DB References</strong><br> <em>This
+ submenu contains options for accessing any of the database
+ services that Jalview is aware of (e.g. DAS sequence servers and
+ the WSDBFetch service provided by the EBI) to verify sequence
+ start/end positions and retrieve all database cross references
+ and PDB ids associated with all or just the selected sequences
+ in the alignment.
+ <ul>
+ <li>'Retrieve full Sequence' - when checked, Jalview will
+ retrieve the full sequence for any accessions associated
+ with sequences in the alignment. <br> <strong>Note:
+ This could cause out of memory errors when working with
+ genomic sequence records !</strong><br> <strong>Added
+ in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the
+ EBI databases plus any active DAS sequence sources<</li>
+ </ul> Other submenus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em></li>
+ </ul>
+ <p>Selecting items from the following submenus will start a remote
+ service on compute facilities at the University of Dundee, or
+ elsewhere. You need a continuous network connection in order to use
+ these services through Jalview.</p>
+ <ul>
+ <li><strong>Alignment</strong><br />
+ <em> Align the currently selected sequences or all sequences in
+ the alignment, or re-align unaligned sequences to the aligned
+ sequences. Entries in this menu provide access to the various
+ alignment programs supported by <a
+ href="../webServices/JABAWS.html"
+ >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
+ Sequence Alignment webservice client</a> entry for more
+ information.
+ </em></li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <ul>
+ <li><strong>JPred Secondary Structure Prediction</strong><br>
+ <em>Secondary structure prediction by network consensus.
+ See the <a href="../webServices/jnet.html">Jpred3</a> client
+ entry for more information. The behaviour of this
+ calculation depends on the current selection:
+ <ul>
+ <li>If nothing is selected, and the displayed
+ sequences appear to be aligned, then a JNet prediction
+ will be run for the first sequence in the alignment,
+ using the current alignment. Otherwise the first
+ sequence will be submitted for prediction.</li>
+ <li>If just one sequence (or a region on one
+ sequence) has been selected, it will be submitted to the
+ automatic JNet prediction server for homolog detection
+ and prediction.</li>
+ <li>If a set of sequences are selected, and they
+ appear to be aligned, then the alignment will be used
+ for a Jnet prediction on the <strong>first</strong>
+ sequence in the set (that is, the one that appears first
+ in the alignment window).
+ </li>
+ </ul>
+ </em>
+ </ul></li>
+ <li><strong>Analysis</strong><br />
+ <ul>
+ <li><strong>Multi-Harmony</strong><br> <em>Performs
+ functional residue analysis on a protein family alignment
+ with sub-families defined on it. See the <a
+ href="../webServices/shmr.html"
+ >Multi-Harmony service</a> entry for more information.
+ </em></li>
+ </ul></li>
+ </ul>
+</body>
+</html>
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