-<html>\r
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-<body>\r
-Web service \r
-</body>\r
-</html>\r
+ <html>
+ <head><title>Web Services</title></head>
+ <body>
+ <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/seqfetcher.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></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>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>
+ </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
+ 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>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