help/html/menus/wsmenu.html

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   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   4  * Copyright (C) 2014 The Jalview Authors
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  20 <head><title>Web Service Menu</title></head>
  21
  22 <body>
  23                 <p><strong>Web Service Menu</strong><br /> <em>This menu
  24                                 is dynamic, and may contain user-defined web service entries in
  25                                 addition to any of the following ones:</em>
  26                         <ul>
  27                                 <li><strong>Fetch DB References</strong><br> <em>This
  28                                                 will use any of the database services that Jalview is aware of
  29                                                 (e.g. DAS sequence servers and the WSDBFetch service provided by
  30                                                 the EBI) to verify the sequence and retrieve all database cross
  31                                                 references and PDB ids associated with all or just the selected
  32                                                 sequences in the alignment. <br />'Standard Databases' will check
  33                                                 sequences against the EBI databases plus any active DAS sequence
  34                                                 sources, or you can verify against a specific source from one of
  35                                                 the sub-menus.</em><br></li>
  36                                 <li><strong>Envision2 Services</strong><br /><em> Submits one or
  37                                         more sequences, sequence IDs or database references to analysis
  38                                         workflows provided by the <a
  39                                         href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
  40                                                 application</a>. This allows Jalview users to easily access the EnCore
  41                                         network of databases and analysis services developed by members of
  42                                         <a href="http://www.enfin.org">ENFIN</a></em>.</li>
  43                         </ul>
  44                         <p>Selecting items from the following submenus will start a
  45                                 remote service on compute facilities at the University of Dundee, or
  46                                 elsewhere. You need a continuous network connection in order to use
  47                                 these services through Jalview.
  48                         </p>
  49                         <ul>
  50                                 <li><strong>Alignment</strong><br /><em> Align the currently
  51                                         selected sequences or all sequences in the alignment, or re-align
  52                                         unaligned sequences to the aligned sequences. Entries in this menu
  53                                         provide access to the various alignment programs supported by <a
  54                                         href="../webServices/JABAWS.html">JABAWS</a>. See the <a
  55                                         href="../webServices/msaclient.html">Multiple Sequence
  56                                                 Alignment webservice client</a> entry for more information.</em></li>
  57                                 <li><strong>Secondary Structure Prediction</strong>
  58                                         <ul>
  59                                                 <li><strong>JPred Secondary Structure Prediction</strong><br>
  60                                                         <em>Secondary structure prediction by network consensus. See
  61                                                                 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
  62                                                                 more information. The behaviour of this calculation depends on
  63                                                                 the current selection:
  64                                                                 <ul>
  65                                                                         <li>If nothing is selected, and the displayed sequences
  66                                                                                 appear to be aligned, then a JNet prediction will be run for
  67                                                                                 the first sequence in the alignment, using the current
  68                                                                                 alignment. Otherwise the first sequence will be submitted for
  69                                                                                 prediction.</li>
  70                                                                         <li>If just one sequence (or a region on one sequence) has
  71                                                                                 been selected, it will be submitted to the automatic JNet
  72                                                                                 prediction server for homolog detection and prediction.</li>
  73                                                                         <li>If a set of sequences are selected, and they appear to
  74                                                                                 be aligned, then the alignment will be used for a Jnet
  75                                                                                 prediction on the <strong>first</strong> sequence in the set
  76                                                                                 (that is, the one that appears first in the alignment window).
  77                                                                         </li>
  78                                                                 </ul> </em>
  79                                         </ul></li>
  80                                 <li><strong>Analysis</strong><br />
  81                                         <ul>
  82                                                 <li><strong>Multi-Harmony</strong><br> <em>Performs
  83                                                                 functional residue analysis on a protein family alignment with
  84                                                                 sub-families defined on it. See the <a
  85                                                                 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
  86                                                                 information.</em>
  87                                                 </li>
  88                                         </ul></li>
  89         </ul>
  90 </body>
  91 </html>