help/html/menus/wsmenu.html

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   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19 <head><title>Web Service Menu</title></head>
  20
  21 <body>
  22                 <p><strong>Web Service Menu</strong><br /> <em>This menu
  23                                 is dynamic, and may contain user-defined web service entries in
  24                                 addition to any of the following ones:</em>
  25                         <ul>
  26                                 <li><strong>Fetch DB References</strong><br> <em>This
  27                                                 will use any of the database services that Jalview is aware of
  28                                                 (e.g. DAS sequence servers and the WSDBFetch service provided by
  29                                                 the EBI) to verify the sequence and retrieve all database cross
  30                                                 references and PDB ids associated with all or just the selected
  31                                                 sequences in the alignment. <br />'Standard Databases' will check
  32                                                 sequences against the EBI databases plus any active DAS sequence
  33                                                 sources, or you can verify against a specific source from one of
  34                                                 the sub-menus.</em><br></li>
  35                                 <li><strong>Envision2 Services</strong><br /><em> Submits one or
  36                                         more sequences, sequence IDs or database references to analysis
  37                                         workflows provided by the <a
  38                                         href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
  39                                                 application</a>. This allows Jalview users to easily access the EnCore
  40                                         network of databases and analysis services developed by members of
  41                                         <a href="http://www.enfin.org">ENFIN</a></em>.</li>
  42                         </ul>
  43                         <p>Selecting items from the following submenus will start a
  44                                 remote service on compute facilities at the University of Dundee, or
  45                                 elsewhere. You need a continuous network connection in order to use
  46                                 these services through Jalview.
  47                         </p>
  48                         <ul>
  49                                 <li><strong>Alignment</strong><br /><em> Align the currently
  50                                         selected sequences or all sequences in the alignment, or re-align
  51                                         unaligned sequences to the aligned sequences. Entries in this menu
  52                                         provide access to the various alignment programs supported by <a
  53                                         href="../webServices/JABAWS.html">JABAWS</a>. See the <a
  54                                         href="../webServices/msaclient.html">Multiple Sequence
  55                                                 Alignment webservice client</a> entry for more information.</em></li>
  56                                 <li><strong>Secondary Structure Prediction</strong>
  57                                         <ul>
  58                                                 <li><strong>JPred Secondary Structure Prediction</strong><br>
  59                                                         <em>Secondary structure prediction by network consensus. See
  60                                                                 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
  61                                                                 more information. The behaviour of this calculation depends on
  62                                                                 the current selection:
  63                                                                 <ul>
  64                                                                         <li>If nothing is selected, and the displayed sequences
  65                                                                                 appear to be aligned, then a JNet prediction will be run for
  66                                                                                 the first sequence in the alignment, using the current
  67                                                                                 alignment. Otherwise the first sequence will be submitted for
  68                                                                                 prediction.</li>
  69                                                                         <li>If just one sequence (or a region on one sequence) has
  70                                                                                 been selected, it will be submitted to the automatic JNet
  71                                                                                 prediction server for homolog detection and prediction.</li>
  72                                                                         <li>If a set of sequences are selected, and they appear to
  73                                                                                 be aligned, then the alignment will be used for a Jnet
  74                                                                                 prediction on the <strong>first</strong> sequence in the set
  75                                                                                 (that is, the one that appears first in the alignment window).
  76                                                                         </li>
  77                                                                 </ul> </em>
  78                                         </ul></li>
  79                                 <li><strong>Analysis</strong><br />
  80                                         <ul>
  81                                                 <li><strong>Multi-Harmony</strong><br> <em>Performs
  82                                                                 functional residue analysis on a protein family alignment with
  83                                                                 sub-families defined on it. See the <a
  84                                                                 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
  85                                                                 information.</em>
  86                                                 </li>
  87                                         </ul></li>
  88         </ul>
  89 </body>
  90 </html>