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-<head>
-<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>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff