help/html/webServices/index.html

   1         <html>\r
   2         <head><title>Web Services</title></head>\r
   3         <body>\r
   4         <p><strong>Web services</strong></p>\r
   5         \r
   6 <p>A variety of web services are available from the Alignment window's <strong> \r
   7   Web Service</strong> menu. </p>\r
   8             <p>Jalview's distributed computations are SOAP based services exposing\r
   9               protein sequence alignment and secondary structure prediction programs. These services actually run\r
  10                 on the cluster based in the School of Life Sciences, University of\r
  11                   Dundee, and are maintained by the Barton group.\r
  12                   </p>\r
  13                   <p><strong>Web Service Dialog Box</strong></p>\r
  14 <img src="clwqueued.gif">\r
  15 <p>\r
  16                   This dialog box is displayed when a web service job\r
  17                   is submitted. It gives the name of the service and\r
  18                   any method citation information, and monitors the\r
  19                   progress of the calculation. The cancel button will\r
  20                   permanently cancel the job, but this is only\r
  21                   possible for some services.\r
  22                   </p>\r
  23                   <p>Current services:\r
  24                   <ul><a href="msaclient.html"><strong>Multiple\r
  25                   Sequence Alignment Services</strong></a><ul>\r
  26                   <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>\r
  27                   The clustal W service remains one of the more\r
  28                   popular Jalview features.\r
  29                   </li>\r
  30                   <li><a href="muscle.html">Muscle Multiple Alignment</a><br>\r
  31                   High Quality and High Throughput multiple alignments of proteins. This\r
  32                   method can sometimes be more accurate than ClustalW when dealing with\r
  33                   diverse sets of sequences.\r
  34                   </li>\r
  35                   <li><a href="mafft.html">MAFFT</a><br>\r
  36                   Multiple Alignment with Fast Fourier Transforms -\r
  37                   a highly accurate and high throughput dna and amino\r
  38                   acid alignment method, performing at least as well\r
  39                   as ClustalW and Muscle.\r
  40                   </li>\r
  41                   </ul>                  \r
  42                   </li>\r
  43                   <li><strong>Secondary Structure Prediction</strong>\r
  44                   <ul>\r
  45                   <li><a href="jnet.html">JNet</a><br>This is a front end to the existing <a\r
  46                   href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet\r
  47                   www server</a> allowing single sequence or profile\r
  48                   based prediction.\r
  49                   </li>\r
  50                   </ul>\r
  51                   </li>\r
  52                   </ul>\r
  53                   </p>\r
  54                   <p>Watch this space! These are some of the services\r
  55                   planned to be released soon:<ul>\r
  56                   <li>Repeat analysis\r
  57                   </li>\r
  58                   <li>Remote Homology Detection<br>\r
  59                   </li>\r
  60                   </ul>\r
  61                   In the future, Jalview will also be able to new discover services\r
  62                   dynamically, and distribute expensive analysis functions like <a\r
  63                   href="../calculations/pca.html">PCA</a> to the Dundee machines.</p>\r
  64 </body>\r
  65 </html>\r