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Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues

Anand, B and Gowri, VS and Srinivasan, N (2005) Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues. In: Bioinformatics, 21 (12). pp. 2821-2826.

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Abstract

MOTIVATION: Position specific scoring matrices (PSSMs) corresponding to aligned sequences of homologous proteins are commonly used in homology detection. A PSSM is generated on the basis of one of the homologues as a reference sequence, which is the query in the case of PSI-BLAST searches. The reference sequence is chosen arbitrarily while generating PSSMs for reverse BLAST searches. In this work we demonstrate that the use of multiple PSSMs corresponding to a given alignment and variable reference sequences is more effective than using traditional single PSSMs and hidden Markov models. RESULTS: Searches for proteins with known 3-D structures have been made against three databases of protein family profiles corresponding to known structures: (1) One PSSM per family; (2) multiple PSSMs corresponding to an alignment and variable reference sequences for every family; and (3) hidden Markov models. A comparison of the performances of these three approaches suggests that the use of multiple PSSMs is most effective.

Item Type: Journal Article
Additional Information: The Copyright belongs to Oxford University Press.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 01 Mar 2006
Last Modified: 27 Aug 2008 11:46
URI: http://eprints.iisc.ernet.in/id/eprint/5642

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