3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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>
28 <li><strong>Fetch DB References</strong><br> <em>This
29 submenu contains options for accessing any of the database services
30 that Jalview is aware of (e.g. DAS sequence servers and the
31 WSDBFetch service provided by the EBI) to verify sequence start/end
32 positions and retrieve all database cross references and PDB ids
33 associated with all or just the selected sequences in the alignment.
35 <li>'Retrieve full Sequence' - when checked, Jalview will
36 retrieve the full sequence for any accessions associated with
37 sequences in the alignment. <br> <strong>Note: This
38 could cause out of memory errors when working with genomic
39 sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
41 <li>'Standard Databases' will check sequences against the EBI
42 databases plus any active DAS sequence sources<</li>
43 </ul> Other submenus allow you to pick a specific source to query -
44 sources are listed alphabetically according to their nickname.
48 <p>Selecting items from the following submenus will start a
49 remote service on compute facilities at the University of Dundee, or
50 elsewhere. You need a continuous network connection in order to use
51 these services through Jalview.
54 <li><strong>Alignment</strong><br /><em> Align the currently
55 selected sequences or all sequences in the alignment, or re-align
56 unaligned sequences to the aligned sequences. Entries in this menu
57 provide access to the various alignment programs supported by <a
58 href="../webServices/JABAWS.html">JABAWS</a>. See the <a
59 href="../webServices/msaclient.html">Multiple Sequence
60 Alignment webservice client</a> entry for more information.</em></li>
61 <li><strong>Secondary Structure Prediction</strong>
63 <li><strong>JPred Secondary Structure Prediction</strong><br>
64 <em>Secondary structure prediction by network consensus. See
65 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
66 more information. The behaviour of this calculation depends on
67 the current selection:
69 <li>If nothing is selected, and the displayed sequences
70 appear to be aligned, then a JNet prediction will be run for
71 the first sequence in the alignment, using the current
72 alignment. Otherwise the first sequence will be submitted for
74 <li>If just one sequence (or a region on one sequence) has
75 been selected, it will be submitted to the automatic JNet
76 prediction server for homolog detection and prediction.</li>
77 <li>If a set of sequences are selected, and they appear to
78 be aligned, then the alignment will be used for a Jnet
79 prediction on the <strong>first</strong> sequence in the set
80 (that is, the one that appears first in the alignment window).
84 <li><strong>Analysis</strong><br />
86 <li><strong>Multi-Harmony</strong><br> <em>Performs
87 functional residue analysis on a protein family alignment with
88 sub-families defined on it. See the <a
89 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more