-<html>\r
-<head><title>Web Service Menu</title></head>\r
-\r
-<body>\r
-<p><strong>Web Service Menu</strong></p>\r
-<p><strong><br>\r
- </strong> <em>Selecting one of the following menu items starts a remote service \r
- on compute facilities at the University of Dundee. You need a continuous network \r
- connection in order to use these services through Jalview. </em> </p>\r
-<ul>\r
- <li><strong>Alignment</strong> \r
- <ul>\r
- <li><strong>ClustalW Multiple Sequence Alignment</strong><br>\r
- <em> Submits all, or just the currently selected sequences for alignment \r
- with clustal W.</em></li>\r
- <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>\r
- <em> Submits the alignment or currently selected region for re-alignment \r
- with clustal W. Use this if you have added some new sequences to an existing \r
- alignment.</em></li>\r
- <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
- <em> Submits all, or jut the currently selected sequences for alignment \r
- using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Secondary Structure Prediction</strong> \r
- <ul>\r
- <li><strong>JPred Secondary Structure Prediction</strong><br>\r
- <em>Secondary structure prediction by network consensus. The behaviour \r
- of this calculation depends on the current selection: </em></li>\r
- <li><em>If nothing is selected, and the displayed sequences appear to be \r
- aligned, then a JNet prediction will be run for the first sequence in \r
- the alignment, using the current alignment. Otherwise the first sequence \r
- will be submitted for prediction. </em></li>\r
- <li><em>If just one sequence (or a region on one sequence) has been selected, \r
- it will be submitted to the automatic JNet prediction server for homolog \r
- detection and prediction. </em></li>\r
- <li><em>If a set of sequences are selected, and they appear to be aligned, \r
- then the alignment will be used for a Jnet prediction on the <strong>first</strong> \r
- sequence in the set (that is, the one that appears first in\r
- the alignment window). </em> </li>\r
- </ul>\r
- </li>\r
-</ul>\r
-<p><strong> </strong></p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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
+ will use 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 the sequence and retrieve all database cross
+ references and PDB ids associated with all or just the selected
+ sequences in the alignment. <br />'Standard Databases' will check
+ sequences against the EBI databases plus any active DAS sequence
+ sources, or you can verify against a specific source from one of
+ the sub-menus.</em><br></li>
+ <li><strong>Envision2 Services</strong><br /><em> Submits one or
+ more sequences, sequence IDs or database references to analysis
+ workflows provided by the <a
+ href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
+ application</a>. This allows Jalview users to easily access the EnCore
+ network of databases and analysis services developed by members of
+ <a href="http://www.enfin.org">ENFIN</a></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>Sequence Harmony Multi-Relief</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">SHMR client</a> entry for more
+ information.</em>
+ </li>
+ </ul></li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff