Nucleic Acids Research Advance Access originally published online on October 26, 2006
Nucleic Acids Research 2006 34(20):5966-5973; doi:10.1093/nar/gkl731
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Nucleic Acids Research, 2006, Vol. 34, No. 20 5966-5973
Published by Oxford University Press 2006
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
National Center for Biotechnology Information, National Library of Medicine NIH, DHHS, Bethesda, MD 20894, USA
*To whom correspondence should be addressed. Tel: +301 435 7803; Fax: +301 480 2288; Email: altschul{at}ncbi.nlm.nih.gov
Received July 27, 2006. Revised September 15, 2006. Accepted September 21, 2006.
Protein sequence database search programs may be evaluated both for their retrieval accuracy—the ability to separate meaningful from chance similarities—and for the accuracy of their statistical assessments of reported alignments. However, methods for improving statistical accuracy can degrade retrieval accuracy by discarding compositional evidence of sequence relatedness. This evidence may be preserved by combining essentially independent measures of alignment and compositional similarity into a unified measure of sequence similarity. A version of the BLAST protein database search program, modified to employ this new measure, outperforms the baseline program in both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set.
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