-<html>\r
-\r
-<body>\r
-<p><strong>Web services </strong></p>\r
-<p>Originally Jalview used SRS server to retrieve sequence features for a given \r
- alignment. In addition certain remote alignment programs could be called from \r
- the Jalview interface and the results displayed in a new alignment panel. </p>\r
-<p>The main emphasis of the current development of the Jalview Project is to implement \r
- various sequence alignment programs, tree analysis, PCA algorithms on a large \r
- cluster based witihin the Barton Group. Jalview will be able to call these remote \r
- procedures without the user having to install any new software. <br>\r
- The main advantage of using these remote web services is that the computing \r
- power available is much greater than that of the users work station.</p>\r
+ <html>\r
+ <head><title>Web Services</title></head>\r
+ <body>\r
+ <p><strong>Web services</strong></p>\r
+ \r
+<p>A variety of web services are available from the Alignment window's <strong> \r
+ Web Service</strong> menu. </p>\r
+ <p>Jalview's distributed computations are SOAP based services exposing\r
+ protein sequence alignment and secondary structure prediction programs. These services actually run\r
+ on the cluster based in the School of Life Sciences, University of\r
+ Dundee, and are maintained by the Barton group.\r
+ </p>\r
+ <p><strong>Web Service Dialog Box</strong></p>\r
+<img src="clwqueued.gif">\r
+<p>\r
+ This dialog box is displayed when a web service job\r
+ is submitted. It gives the name of the service and\r
+ any method citation information, and monitors the\r
+ progress of the calculation. The cancel button will\r
+ permanently cancel the job, but this is only\r
+ possible for some services.\r
+ </p>\r
+ <p>Current services:\r
+ <ul><a href="msaclient.html"><strong>Multiple\r
+ Sequence Alignment Services</strong></a><ul>\r
+ <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>\r
+ The clustal W service remains one of the more\r
+ popular Jalview features.\r
+ </li>\r
+ <li><a href="muscle.html">Muscle Multiple Alignment</a><br>\r
+ High Quality and High Throughput multiple alignments of proteins. This\r
+ method can sometimes be more accurate than ClustalW when dealing with\r
+ diverse sets of sequences.\r
+ </li>\r
+ <li><a href="mafft.html">MAFFT</a><br>\r
+ Multiple Alignment with Fast Fourier Transforms -\r
+ a highly accurate and high throughput dna and amino\r
+ acid alignment method, performing at least as well\r
+ as ClustalW and Muscle.\r
+ </li>\r
+ </ul> \r
+ </li>\r
+ <li><strong>Secondary Structure Prediction</strong>\r
+ <ul>\r
+ <li><a href="jnet.html">JNet</a><br>This is a front end to the existing <a\r
+ href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet\r
+ www server</a> allowing single sequence or profile\r
+ based prediction.\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ </ul>\r
+ </p>\r
+ <p>Watch this space! These are some of the services\r
+ planned to be released soon:<ul>\r
+ <li>Repeat analysis\r
+ </li>\r
+ <li>Remote Homology Detection<br>\r
+ </li>\r
+ </ul>\r
+ In the future, Jalview will also be able to new discover services\r
+ dynamically, and distribute expensive analysis functions like <a\r
+ href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff