-<p><strong>Web services</strong></p>
-
-<p>Jalview includes clients for a variety of web services for both
-bioinformatic data retrieval and analysis.
-<ul>
- <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
- utilises web services for sequence, alignment and structure retrieval
- provided by the European Bioinformatics Institute (EBI) and Distributed
- Annotation System servers that are capable of serving sequences.</li>
- <li>The <a href="../features/dasfeatures.html">DAS Feature
- Fetcher</a> enables the retrieval and visualization of features from DAS
- annotation sources</li>
- <li>The <a href="dbreffetcher.html">Database Reference Fetcher</a>
- transfers database references from records available from DAS or the
- public sequence databases.</li>
- <li>The <strong>Web Services</strong> menu in each alignment
- window also provides access to the following:
- <ul>
- <li>Jalview SOAP Web Services for sequence alignment and
- secondary structure prediction based at the University of Dundee.</li>
- <li>Services for submitting IDs and sequences to external
- bioinformatics services such as <a href="#envision2">Envision2</a>.</li>
- <li>Programs for multiple sequence alignment, made available <em>via</em>
- <a href="JABAWS.html">Java Bioinformatic Analysis Web Service
- (JABAWS)</a> servers.</li>
- </ul>
- The <a href="webServicesPrefs.html">Web Services Preference panel</a>
- controls the display and appearance of the submission and analysis
- services in the <strong>Web Services</strong> menu.</li>
- <li>If Jalview encounters problems accessing any services, it may
- display a <a href="webServicesPrefs.html#wswarnings">warning dialog
- box</a> (this can be turned off using the web services preferences tab).</li>
-</ul>
-</p>
-<p><strong>More about Jalview's Web Services</strong> <br>
-Jalview's distributed computations are SOAP based services exposing
-protein sequence alignment and secondary structure prediction programs.
-These services actually run on the cluster based in the School of Life
-Sciences, University of Dundee, and are maintained by the Barton group.</p>
-<p><strong><a name="envision2">Envision2 Services</a></strong></p>
-<p>Since version 2.5, Jalview has included a client to enable the
-user to submit one or more sequences or sequence IDs 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 ENFIN (<a
- href="http://www.enfin.org">www.enfin.org</a>).</p>
-<br />
-<p><strong>Web Service Dialog Box</strong></p>
-<img src="clwqueued.gif">
-<p>This dialog box is displayed when a web service job is submitted.
-It gives the name of the service and any method citation information,
-and monitors the progress of the calculation. The cancel button will
-permanently cancel the job, but this is only possible for some services.
-</p>
-<p>Current services:
-<ul>
- <a href="msaclient.html"><strong>Multiple Sequence
- Alignment Services</strong></a>
- <ul>
- <li><a href="clustalw.html">ClustalW Multiple Alignment and
- re-alignment</a><br>
- The clustal W service remains one of the more popular Jalview
- features.</li>
- <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
- High Quality and High Throughput multiple alignments of proteins. This
- method can sometimes be more accurate than ClustalW when dealing with
- diverse sets of sequences.</li>
- <li><a href="mafft.html">MAFFT</a><br>
- Multiple Alignment with Fast Fourier Transforms - a highly accurate
- and high throughput dna and amino acid alignment method, performing at
- least as well as ClustalW and Muscle.</li>
- <li>Other alignment methods are also available via <a
- href="JABAWS.html">JABAWS</a>. For more information about a
- particular service, see the documentation available via the <a
- href="webServicesParams.html">web services parameter dialog box</a>.</li>
- </ul>
- </li>
- <li><strong>Secondary Structure Prediction</strong>
- <ul>
- <li><a href="jnet.html">JNet</a><br>
- This is a front end to the <a
- href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet www server</a>
- allowing single sequence or profile based prediction.</li>
- </ul>
- </li>
-</ul>
-</p>