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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
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* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
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+ * 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
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--->
-<head><title>Web Service Menu</title></head>
+ * 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></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>
+ <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>
- </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>
+ <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>
- <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>
+ <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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