-<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>MAFFT Multiple Sequence Alignment</strong><br>\r
- <em>Submits all, or just the currently selected region for alignment with \r
- MAFFT. </em> </li>\r
- <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
- <em> Submits all, or just 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 the alignment \r
- 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)
+ * 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></p>
+<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/>
+ 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>.
+ </li>
+ </ul>
+ </strong> <em>Selecting one of the following menu items starts a remote service
+ on compute facilities at the University of Dundee. You need a continuous network
+ connection in order to use these services through Jalview. </em> </p>
+ <ul>
+ <li><strong>Alignment</strong>
+ <ul>
+ <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
+ <em> Submits all, or just the currently selected sequences for alignment
+ with clustal W.</em></li>
+ <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
+ <em> Submits the alignment or currently selected region for re-alignment
+ with clustal W. This enables you to align more sequences to an existing alignment.</em></li>
+ <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
+ <em>Submits all, or just the currently selected region for alignment with
+ MAFFT. </em> </li>
+ <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
+ <em> Submits all, or just the currently selected sequences for alignment
+ using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>
+ </ul>
+ </li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <ul>
+ <li><strong>JPred Secondary Structure Prediction</strong><br>
+ <em>Secondary structure prediction by network consensus. The behaviour
+ of this calculation depends on the current selection: </em></li>
+ <li><em>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. </em></li>
+ <li><em>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. </em></li>
+ <li><em>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). </em> </li>
+ </ul>
+ </li>
+</ul>
+<p><strong> </strong></p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff