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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
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+ * Jalview is free software: you can redistribute it and/or
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+ * of the License, or (at your option) any later version.
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+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head><title>Web Service Menu</title></head>
<body>
-<p><strong>Web Service Menu</strong></p>
-<p><strong><br>
- </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>Fetch DB References</strong><br>
- <em>This will use the service WSDBFetch, provided by the EBI, to retrieve all
- uniprot database cross references and PDB ids associated with the selected sequences in
- the alignment if the sequences have valid Uniprot names or accession ids.</em><br>
- </li>
- <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. Use this if you have added some new 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>
+ <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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