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/>.
20 <title>Multi-Group Sequence Harmony and Multi-Relief</title>
23 <strong>Functional residue analysis with Sequence Harmony and
26 The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or SHMR) service (<a
27 href="#shmrref">Brandt, Feenstra and Heringa, 2010</a>) available
28 from the <em>Analysis</em> sub-menu of the alignment window's web
29 services menu provides a method for the identification of significant
30 patterns of <em>sub-family variation</em> amongst the columns of an
34 <strong>Instructions for use</strong><br> The service requires a
35 protein sequence multiple alignment that has been sub-divided into
36 groups containing at least two non-identical protein sequences. An
37 easy way to create groups is to use the built-in <a
38 href="../calculations/tree.html">neighbour-joining or UPGMA tree</a>
39 routines to calculate a tree for the alignment, and then click on the
40 tree to subdivide the alignment.
43 The SHMR service operates on the currently selected visible region(s)
44 of the alignment. Once submitted, a job progress window will display
45 status information about your job, including a URL which allows you to
46 visit the status page on the
47 <a href="http://zeus.few.vu.nl/programs/shmrwww/">IBIVU SHMR server</a>.
49 <p>When the job is complete, Jalview will automatically open a new
50 window containing the alignment and groups that were submitted for
51 analysis, with additional histograms added portraying the SHMR scores
52 for each column of the sub-grouped alignment.</p>
54 If you use this service in your work, please cite :<br /><a name="shmrref"/> Brandt,
55 B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting
56 functional specificity from sequence alignment. <a
57 href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415">Nucleic
58 Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
60 <strong><em>Note:</em></strong> The Multi-Harmony service is implemented with a prototype of Jalview's RESTful
61 web service client introduced in Jalview 2.7. A few bugs remain in this prototype, which we intend to fixed in version 2.7.1.