MulPSSM: a database of multiple position-specific scoring matrices of protein domain families
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 ha...
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Published in | Nucleic acids research Vol. 34; no. suppl-1; pp. D243 - D246 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
01.01.2006
Oxford Publishing Limited (England) |
Subjects | |
Online Access | Get full text |
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Summary: | 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. |
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Bibliography: | local:gkj043 istex:524870C690245EA97F18175368D4384B3D1F0597 To whom correspondence should be addressed. Tel: +91 80 2293 2837; Fax: +91 80 2360 0535; Email: ns@mbu.iisc.ernet.in ark:/67375/HXZ-CJTSPKSX-C ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors |
ISSN: | 0305-1048 1362-4962 |
DOI: | 10.1093/nar/gkj043 |