Anand, B and Gowri, VS and Srinivasan, N (2005) Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues. In: Bioinformatics, 21 (12). pp. 2821-2826.
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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.
| Item Type: | Journal Article |
|---|---|
| Publication: | Bioinformatics |
| Publisher: | Oxford University Press |
| Additional Information: | The Copyright belongs to Oxford University Press. |
| Department/Centre: | Division of Biological Sciences > Molecular Biophysics Unit |
| Date Deposited: | 01 Mar 2006 |
| Last Modified: | 27 Aug 2008 11:46 |
| URI: | http://eprints.iisc.ac.in/id/eprint/5642 |
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