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Bioinformatics Advance Access originally published online on February 27, 2009
Bioinformatics 2009 25(8):1082-1083; doi:10.1093/bioinformatics/btp089
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance

Ankit Agrawal * and Xiaoqiu Huang

Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011-1041, USA

*To whom correspondence should be addressed.


  Abstract

Summary: We present an add-on to BLAST and PSI-BLAST programs to reorder their hits using pairwise statistical significance. Using position-specific substitution matrices to estimate pairwise statistical significance has been recently shown to give promising results in terms of retrieval accuracy, which motivates its use to refine PSI-BLAST results, since PSI-BLAST also constructs a position-specific substitution matrix for the query sequence during the search. The obvious advantage of the approach is more accurate estimates of statistical significance because of pairwise statistical significance, along with the advantage of BLAST/PSI-BLAST in terms of speed.

Availability: The implementation as a C library is freely available at www.cs.iastate.edu/~ankitag/PSIBLAST_PairwiseStatSig.html

Contact: ankitag{at}cs.iastate.edu

Supplementary information: Supplementary data are available at Bionformatics online.

Associate Editor: Alfonso Valencia

Received on November 29, 2008; revised on January 23, 2009; accepted on February 12, 2009

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