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Bioinformatics Advance Access published online on March 29, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti374
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received August 26, 2004
Revised February 14, 2005
Accepted March 2, 2005

Article

Quasi-consensus based comparison of profile hidden Markov models for protein sequences

Robel Y. Kahsay 1, Guoli Wang 2, Guang Gao 1, Li Liao 3*, and Roland Dunbrack 2

1 Delaware Biotechnology Institute, Newark, DE 19715
2 Fox Chase Cancer Center, Philadelphia, PA 19111
3 Delaware Biotechnology Institute, Newark, DE 19715; Department of Computer & Information Sciences, University of Delaware, Newark, DE 19716


  Abstract

A simple approach for sensitive detection of distant relationships among protein families and for sequence-structure alignment via comparison of hidden Markov models based on their quasi-consensus sequences is presented. Using a previously published benchmark dataset, the approach is demonstrated to give better homology detection and yields alignments with improved accuracy in comparison to an existing state-of-the-art dynamic-programming profile-profile comparison method. This method also runs significantly faster and is therefore suitable for a server covering the rapidly increasing structure database. A server based on this method is available at http://liao.cis.udel.edu/website/servers/modmod.


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