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 mul-tiple sequence alignment as a reference. We have shown recently that the use of multiple PSSMs corre-sponding 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 identifymost distinct sequences corresponding to a family. With each one of the distinct sequences as reference, mul-tiplePSSMshavebeengenerated. Thecurrent 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 PSSMsof sequence or structural fami-lies or both. An analysis interface allows display and convenientnavigationof alignments anddomainhits. MulPSSM can be accessed a