+++ /dev/null
-<html>
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- * 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>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 services 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</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">Jpred</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 JPred 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 JPred 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 JPred 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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