help/html/menus/wsmenu.html

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   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   4  * Copyright (C) 2014 The Jalview Authors
   5  *
   6  * This file is part of Jalview.
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   8  * Jalview is free software: you can redistribute it and/or
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  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
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  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
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  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  -->
  22 <head><title>Web Service Menu</title></head>
  23
  24 <body>
  25                 <p><strong>Web Service Menu</strong><br /> <em>This menu
  26                                 is dynamic, and may contain user-defined web service entries in
  27                                 addition to any of the following ones:</em>
  28
  29         <ul>
  30                 <li><strong>Fetch DB References</strong><br> <em>This
  31                                 submenu contains options for accessing any of the database services
  32                                 that Jalview is aware of (e.g. DAS sequence servers and the
  33                                 WSDBFetch service provided by the EBI) to verify sequence start/end
  34                                 positions and retrieve all database cross references and PDB ids
  35                                 associated with all or just the selected sequences in the alignment.
  36                                 <ul>
  37                                         <li>'Retrieve full Sequence' - when checked, Jalview will
  38                                                 retrieve the full sequence for any accessions associated with
  39                                                 sequences in the alignment. <br> <strong>Note: This
  40                                                         could cause out of memory errors when working with genomic
  41                                                         sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
  42                     </li>
  43                                         <li>'Standard Databases' will check sequences against the EBI
  44                                                 databases plus any active DAS sequence sources<</li>
  45                                 </ul> Other submenus allow you to pick a specific source to query -
  46                                 sources are listed alphabetically according to their nickname.
  47                 </em>
  48         </li>
  49         </ul>
  50         <p>Selecting items from the following submenus will start a
  51                                 remote service on compute facilities at the University of Dundee, or
  52                                 elsewhere. You need a continuous network connection in order to use
  53                                 these services through Jalview.
  54                         </p>
  55                         <ul>
  56                                 <li><strong>Alignment</strong><br /><em> Align the currently
  57                                         selected sequences or all sequences in the alignment, or re-align
  58                                         unaligned sequences to the aligned sequences. Entries in this menu
  59                                         provide access to the various alignment programs supported by <a
  60                                         href="../webServices/JABAWS.html">JABAWS</a>. See the <a
  61                                         href="../webServices/msaclient.html">Multiple Sequence
  62                                                 Alignment webservice client</a> entry for more information.</em></li>
  63                                 <li><strong>Secondary Structure Prediction</strong>
  64                                         <ul>
  65                                                 <li><strong>JPred Secondary Structure Prediction</strong><br>
  66                                                         <em>Secondary structure prediction by network consensus. See
  67                                                                 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
  68                                                                 more information. The behaviour of this calculation depends on
  69                                                                 the current selection:
  70                                                                 <ul>
  71                                                                         <li>If nothing is selected, and the displayed sequences
  72                                                                                 appear to be aligned, then a JNet prediction will be run for
  73                                                                                 the first sequence in the alignment, using the current
  74                                                                                 alignment. Otherwise the first sequence will be submitted for
  75                                                                                 prediction.</li>
  76                                                                         <li>If just one sequence (or a region on one sequence) has
  77                                                                                 been selected, it will be submitted to the automatic JNet
  78                                                                                 prediction server for homolog detection and prediction.</li>
  79                                                                         <li>If a set of sequences are selected, and they appear to
  80                                                                                 be aligned, then the alignment will be used for a Jnet
  81                                                                                 prediction on the <strong>first</strong> sequence in the set
  82                                                                                 (that is, the one that appears first in the alignment window).
  83                                                                         </li>
  84                                                                 </ul> </em>
  85                                         </ul></li>
  86                                 <li><strong>Analysis</strong><br />
  87                                         <ul>
  88                                                 <li><strong>Multi-Harmony</strong><br> <em>Performs
  89                                                                 functional residue analysis on a protein family alignment with
  90                                                                 sub-families defined on it. See the <a
  91                                                                 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
  92                                                                 information.</em>
  93                                                 </li>
  94                                         </ul></li>
  95         </ul>
  96 </body>
  97 </html>