title: Strategies for the effective identification of remotely related sequences in multiple PSSM search approach.
abstract: Searches using position specific scoring matrices (PSSMs) have been commonly used in remote homology detection procedures such as PSI-BLAST and RPS-BLAST. A PSSM is generated typically using one of the sequences of a family as the reference sequence. In the case of PSI-BLAST searches the reference sequence is same as the query. Recently we have shown that searches against the database of multiple family-profiles, with each one of the members of the family used as a reference sequence, are more effective than searches against the classical database of single family-profiles. Despite relatively a better overall performance when compared with common sequence-profile matching procedures, searches against the multiple family-profiles database result in a few false positives and false negatives. Here we show that profile length and divergence of sequences used in the construction of a PSSM have major influence on the performance of multiple profile based search approach. We also identify that a simple parameter defined by the number of PSSMs corresponding to a family that is hit, for a query, divided by the total number of PSSMs in the family can distinguish effectively the true positives from the false positives in the multiple profiles search approach.
authors: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
authors: V S
authors: VS
authors: Gowri
authors: K G
authors: KG
authors: Tina
authors: O
authors: O
authors: Krishnadev
authors: N
authors: N
authors: Srinivasan
mesh_terms: D000595:Amino Acid Sequence; D030562:Databases, Protein / Q000145:classification; D012680:Sensitivity and Specificity; D017386:Sequence Homology, Amino Acid