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Nucleic Acids Research 2006 34(Database Issue):D243-D246; doi:10.1093/nar/gkj043
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Nucleic Acids Research, 2006, Vol. 34, Database issue D243-D246
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

MulPSSM: a database of multiple position-specific scoring matrices of protein domain families

V. S. Gowri1, O. Krishnadev1, C. S. Swamy1,2 and N. Srinivasan1,*

1Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012, India 2National Centre for Biological Sciences GKVK Campus, Bangalore 560065, India

*To whom correspondence should be addressed. Tel: +91 80 2293 2837; Fax: +91 80 2360 0535; Email: ns{at}mbu.iisc.ernet.in

Received August 15, 2005. Revised October 3, 2005. Accepted October 3, 2005.

Representation of multiple sequence alignments of protein families in terms of position-specific scoring matrices (PSSMs) is commonly used in the detection of remote homologues. A PSSM is generated with respect to one of the sequences involved in the multiple sequence alignment as a reference. We have shown recently that the use of multiple PSSMs corresponding to an alignment, with several sequences in the family used as reference, improves the sensitivity of the remote homology detection dramatically. MulPSSM contains PSSMs for a large number of sequence and structural families of protein domains with multiple PSSMs for every family. The approach involves use of a clustering algorithm to identify most distinct sequences corresponding to a family. With each one of the distinct sequences as reference, multiple PSSMs have been generated. The current release of MulPSSM contains ~33 000 and ~38 000 PSSMs corresponding to 7868 sequence and 2625 structural families. A RPS_BLAST interface allows sequence search against PSSMs of sequence or structural families or both. An analysis interface allows display and convenient navigation of alignments and domain hits. MulPSSM can be accessed at http://crick.mbu.iisc.ernet.in/~mulpssm.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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