Nucleic Acids Research Advance Access originally published online on June 21, 2007
Nucleic Acids Research 2007 35(Web Server issue):W495-W498; doi:10.1093/nar/gkm406
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W495-W498
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Sequence harmony: detecting functional specificity from alignments
1Centre for Integrative Bioinformatics VU (IBIVU) and 2Institute of Molecular Cell Biology, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands
*To whom correspondence should be addressed. Tel: +31 20 598 7649; Fax: +31 20 598 7653; Email: heringa{at}few.vu.nl
Received January 31, 2007. Revised April 5, 2007. Accepted May 3, 2007.
Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww.
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