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Nucleic Acids Research, 2001, Vol. 29, No. 14 2994-3005
© 2001 Oxford University Press
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
PSI-BLAST is an iterative program to search a database for proteins with distant similarity to a query sequence. We investigated over a dozen modifications to the methods used in PSI-BLAST, with the goal of improving accuracy in finding true positive matches. To evaluate performance we used a set of 103 queries for which the true positives in yeast had been annotated by human experts, and a popular measure of retrieval accuracy (ROC) that can be normalized to take on values between 0 (worst) and 1 (best). The modifications we consider novel improve the ROC score from 0.758 ± 0.005 to 0.895 ± 0.003. This does not include the benefits from four modifications we included in the ‘baseline’ version, even though they were not implemented in PSI-BLAST version 2.0. The improvement in accuracy was confirmed on a small second test set. This test involved analyzing three protein families with curated lists of true positives from the non-redundant protein database. The modification that accounts for the majority of the improvement is the use, for each database sequence, of a position-specific scoring system tuned to that sequence’s amino acid composition. The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST.
* To whom correspondence should be addressed. Tel: +1 301 435 5884; Fax: +1 301 480 2918; Email: schaffer{at}helix.nih.gov
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S. Richardt, D. Lang, R. Reski, W. Frank, and S. A. Rensing PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins Plant Physiology, April 1, 2007; 143(4): 1452 - 1466. [Abstract] [Full Text] [PDF]
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K. L. Visick, T. M. O'Shea, A. H. Klein, K. Geszvain, and A. J. Wolfe The Sugar Phosphotransferase System of Vibrio fischeri Inhibits both Motility and Bioluminescence J. Bacteriol., March 15, 2007; 189(6): 2571 - 2574. [Abstract] [Full Text] [PDF]
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P. Fariselli, I. Rossi, E. Capriotti, and R. Casadio The WWWH of remote homolog detection: The state of the art Brief Bioinform, March 1, 2007; 8(2): 78 - 87. [Abstract] [Full Text] [PDF]
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M. Suzuki, H. H.-Y. Wang, and D. R. McCarty Repression of the LEAFY COTYLEDON 1/B3 Regulatory Network in Plant Embryo Development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 Genes Plant Physiology, February 1, 2007; 143(2): 902 - 911. [Abstract] [Full Text] [PDF]
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C. Zaros, J.-F. Briand, Y. Boulard, S. Labarre-Mariotte, M. C. Garcia-Lopez, P. Thuriaux, and F. Navarro Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases Nucleic Acids Res., January 28, 2007; 35(2): 634 - 647. [Abstract] [Full Text] [PDF]
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D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, et al. Database resources of the National Center for Biotechnology Information Nucleic Acids Res., January 12, 2007; 35(suppl_1): D5 - D12. [Abstract] [Full Text] [PDF]
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