3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
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.
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.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>Web Service Menu</title></head>
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>
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>
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.
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>
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:
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
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).
79 <li><strong>Analysis</strong><br />
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