+++ /dev/null
-<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>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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