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 earlier that 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 [1,2]. MulPSSM contains PSSMs for a large number of sequence and structural families of protein domains with multiple PSSMs for every family [3]. 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.



protein sequence protein domains and classification

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