| Strategies for the effective identification of remotely related sequences in multiple PSSM search approach. | |
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MedLine Citation:
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PMID: 17380509 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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. |
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Authors:
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V S Gowri; K G Tina; O Krishnadev; N Srinivasan |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Proteins Volume: 67 ISSN: 1097-0134 ISO Abbreviation: Proteins Publication Date: 2007 Jun |
Date Detail:
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Created Date: 2007-05-11 Completed Date: 2007-06-07 Revised Date: 2007-08-13 |
Medline Journal Info:
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Nlm Unique ID: 8700181 Medline TA: Proteins Country: United States |
Other Details:
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Languages: eng Pagination: 789-94 Citation Subset: IM |
Copyright Information:
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2007 Wiley-Liss, Inc. |
Affiliation:
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Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Amino Acid Sequence Databases, Protein* / classification Sensitivity and Specificity Sequence Homology, Amino Acid |
| Grant Support | |
ID/Acronym/Agency:
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//Wellcome Trust |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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