<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
<p>Jalview includes clients for a variety of web services for both
bioinformatic data retrieval and analysis.
<ul>
- <li>The <a href="../features/seqfetcher.html">Sequence Fetcher</a>
+ <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 DAS Feature Fetcher enables the retrieval and
- visualization of features from DAS annotation sources</li>
- <li>Jalview SOAP Web Services for sequence and alignment analysis
- are provided by the University of Dundee, and are available from the
- Alignment window's <strong> Web Service</strong> menu.</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>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>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>Jalview 2.5 includes 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 members of <a href="http://www.enfin.org">ENFIN</a>.</p>
-<br/>
+<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.
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 existing <a
+ 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>
-<!-- <p>Watch this space! These are some of the services
- planned to be released soon:<ul>
- <li>More alignment services: PROBCONS, T-COFFEE</li>
- <li>Repeat analysis
- </li>
- <li>Remote Homology Detection<br>
- </li>
- </ul>
- In the future, Jalview will also be able to new discover services
- dynamically, and distribute expensive analysis functions like <a
- href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>-->
+
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff