Name
Title | ||
|---|---|---|
Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues. |
Abstract | ||
|---|---|---|
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.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.ns@mbu.iisc.ernet.in. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1093/bioinformatics/bti432 | Bioinformatics |
Keywords | Field | DocType |
sequence alignment,reference sequence,known structure,3-d structure,protein family profile,homology detection,traditional single pssms,psi-blast search,hidden markov model,multiple profile,multiple pssms,remote homologues,effective detection,variable reference sequence | Sequence alignment,Position-Specific Scoring Matrices,Protein family,Computer science,Protein superfamily,Bioinformatics,Hidden Markov model,Insertion sequence,Reference genome | Journal |
Volume | Issue | ISSN |
21 | 12 | 1367-4803 |
Citations | PageRank | References |
8 | 0.60 | 8 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| B. Anand | 1 | 27 | 4.03 |
| V. S. Gowri | 2 | 49 | 6.43 |
| N Srinivasan | 3 | 8 | 0.60 |