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Updated: Aug 18, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues
B Anand1, V S Gowri, N Srinivasan
1Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
Motivation:
Position specific scoring matrices (PSSMs) corresponding to aligned sequences of homologous proteins are commonly used in homology detection. A PSSM is generated on the basis of one of the homologues as a reference sequence, which is the query in the case of PSI-BLAST searches. The reference sequence is chosen arbitrarily while generating PSSMs for reverse BLAST searches. In this work we demonstrate that the use of multiple PSSMs corresponding to a given alignment and variable reference sequences is more effective than using traditional single PSSMs and hidden Markov models.
Results:
Searches for proteins with known 3-D structures have been made against three databases of protein family profiles corresponding to known structures: (1) One PSSM per family; (2) multiple PSSMs corresponding to an alignment and variable reference sequences for every family; and (3) hidden Markov models. A comparison of the performances of these three approaches suggests that the use of multiple PSSMs is most effective.
Contact:
ns@mbu.iisc.ernet.in.
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