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Bioinformatics Advance Access originally published online on October 6, 2007
Bioinformatics 2007 23(22):3095-3097; doi:10.1093/bioinformatics/btm492
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

HMM-Kalign: a tool for generating sub-optimal HMM alignments

Emmanuelle Becker *, Aurélie Cotillard , Vincent Meyer , Hocine Madaoui and Raphaël Guérois *

CEA, iBiTecS, URA 2096, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, Gif sur Yvette, F-91191 France

*To whom correspondence should be addressed.


  Abstract

Summary: Recent development of strategies using multiple sequence alignments (MSA) or profiles to detect remote homologies between proteins has led to a significant increase in the number of proteins whose structures can be generated by comparative modeling methods. However, prediction of the optimal alignment between these highly divergent homologous proteins remains a difficult issue. We present a tool based on a generalized Viterbi algorithm that generates optimal and sub-optimal alignments between a sequence and a Hidden Markov Model. The tool is implemented as a new function within the HMMER package called hmmkalign.

Availability:http://www-spider.cea.fr/Groups/hk3039/view.html

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on April 10, 2007; revised on September 10, 2007; accepted on September 26, 2007

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