3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
4 * Copyright (C) 2014 The Jalview Authors
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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <head><title>Web Service Menu</title></head>
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>
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>
37 <p>Selecting items from the following submenus will start a
38 remote service on compute facilities at the University of Dundee, or
39 elsewhere. You need a continuous network connection in order to use
40 these services through Jalview.
43 <li><strong>Alignment</strong><br /><em> Align the currently
44 selected sequences or all sequences in the alignment, or re-align
45 unaligned sequences to the aligned sequences. Entries in this menu
46 provide access to the various alignment programs supported by <a
47 href="../webServices/JABAWS.html">JABAWS</a>. See the <a
48 href="../webServices/msaclient.html">Multiple Sequence
49 Alignment webservice client</a> entry for more information.</em></li>
50 <li><strong>Secondary Structure Prediction</strong>
52 <li><strong>JPred Secondary Structure Prediction</strong><br>
53 <em>Secondary structure prediction by network consensus. See
54 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
55 more information. The behaviour of this calculation depends on
56 the current selection:
58 <li>If nothing is selected, and the displayed sequences
59 appear to be aligned, then a JNet prediction will be run for
60 the first sequence in the alignment, using the current
61 alignment. Otherwise the first sequence will be submitted for
63 <li>If just one sequence (or a region on one sequence) has
64 been selected, it will be submitted to the automatic JNet
65 prediction server for homolog detection and prediction.</li>
66 <li>If a set of sequences are selected, and they appear to
67 be aligned, then the alignment will be used for a Jnet
68 prediction on the <strong>first</strong> sequence in the set
69 (that is, the one that appears first in the alignment window).
73 <li><strong>Analysis</strong><br />
75 <li><strong>Multi-Harmony</strong><br> <em>Performs
76 functional residue analysis on a protein family alignment with
77 sub-families defined on it. See the <a
78 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more