<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>
+ <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>
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