Multi-Harmony: detecting functional specificity from sequence alignment.
Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in different protein-protein interactions. A small number of amino acids generally determine functional specificity. The identification of these residues can aid the understanding of protein function and help finding targets for experimental analysis. Here, we present multi-Harmony, an interactive web sever for detecting sub-type-specific sites in proteins starting from a multiple sequence alignment. Combining our Sequence Harmony (SH) and multi-Relief (mR) methods in one web server allows simultaneous analysis and comparison of specificity residues; furthermore, both methods have been significantly improved and extended. SH has been extended to cope with more than two sub-groups. mR has been changed from a sampling implementation to a deterministic one, making it more consistent and user friendly. For both methods Z-scores are reported. The multi-Harmony web server produces a dynamic output page, which includes interactive connections to the Jalview and Jmol applets, thereby allowing interactive analysis of the results. Multi-Harmony is available at http://www.ibi.vu.nl/ programs/shmrwww.
Brandt
Bernd W
BW
Centre for Integrative Bioinformatics, VU University Amsterdam, De Boelelaan 1081A, 1081HV Amsterdam, The Netherlands.
Feenstra
K Anton
KA
Heringa
Jaap
J
D000465:Algorithms; D020407:Internet; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D051785:Smad Proteins / Q000737:chemistry / Q000145:classification; D012984:Software
D051785:Smad Proteins