<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>Multi-Group Sequence Harmony and Multi-Relief</title>
</head>
<body>
- <strong>Functional residue analysis with Sequence Harmony and
- Multi-Relief</strong>
- <p>
- The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or SHMR) service (<a
- href="#shmrref">Brandt, Feenstra and Heringa, 2010</a>) available
- from the <em>Analysis</em> sub-menu of the alignment window's web
- services menu provides a method for the identification of significant
- patterns of <em>sub-family variation</em> amongst the columns of an
- alignment.
- </p>
- <p>
- <strong>Instructions for use</strong><br> The service requires a
- protein sequence multiple alignment that has been sub-divided into
- groups containing at least two non-identical protein sequences. An
- easy way to create groups is to use the built-in <a
- href="../calculations/tree.html">neighbour-joining or UPGMA tree</a>
- routines to calculate a tree for the alignment, and then click on the
- tree to subdivide the alignment.
- </p>
- <p>
- The SHMR service operates on the currently selected visible region(s)
- of the alignment. Once submitted, a job progress window will display
- status information about your job, including a URL which allows you to
- visit the status page on the
- <a href="http://zeus.few.vu.nl/programs/shmrwww/">IBIVU SHMR server</a>.
- </p>
- <p>When the job is complete, Jalview will automatically open a new
- window containing the alignment and groups that were submitted for
- analysis, with additional histograms added portraying the SHMR scores
- for each column of the sub-grouped alignment.</p>
- <p>
- If you use this service in your work, please cite :<br /><a name="shmrref"/> Brandt,
- B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting
- functional specificity from sequence alignment. <a
- href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415">Nucleic
- Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
- <p>
- <strong><em>Note:</em></strong> The Multi-Harmony service is implemented with a prototype of Jalview's RESTful
- 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.
- </ul>
- </p>
+ <strong>Functional residue analysis with Sequence Harmony and
+ Multi-Relief</strong>
+ <p>
+ The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or
+ SHMR) service (<a href="#shmrref">Brandt, Feenstra and Heringa,
+ 2010</a>) available from the <em>Analysis</em> sub-menu of the
+ alignment window's web services menu provides a method for the
+ identification of significant patterns of <em>sub-family
+ variation</em> amongst the columns of an alignment.
+ </p>
+ <p>
+ <strong>Instructions for use</strong><br> The service requires
+ a protein sequence multiple alignment that has been sub-divided into
+ groups containing at least two non-identical protein sequences. An
+ easy way to create groups is to use the built-in <a
+ href="../calculations/tree.html"
+ >neighbour-joining or UPGMA tree</a> routines to calculate a tree for
+ the alignment, and then click on the tree to subdivide the
+ alignment.
+ </p>
+ <p>
+ The SHMR service operates on the currently selected visible
+ region(s) of the alignment. Once submitted, a job progress window
+ will display status information about your job, including a URL
+ which allows you to visit the status page on the <a
+ href="http://zeus.few.vu.nl/programs/shmrwww/"
+ >IBIVU SHMR server</a>.
+ </p>
+ <p>When the job is complete, Jalview will automatically open a new
+ window containing the alignment and groups that were submitted for
+ analysis, with additional histograms added portraying the SHMR
+ scores for each column of the sub-grouped alignment.</p>
+ <p>
+ If you use this service in your work, please cite :<br />
+ <a name="shmrref" /> Brandt, B.W.*, Feenstra, K.A*. and Heringa, J.
+ (2010) Multi-Harmony: detecting functional specificity from sequence
+ alignment. <a
+ href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415"
+ >Nucleic Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
+
+ <p>
+ <strong><em>Note:</em></strong> The Multi-Harmony service is
+ implemented with a prototype of Jalview's RESTful 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.
+ </ul>
+ </p>
</body>
</html>
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