Journal Article

PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance

Ankit Agrawal and Xiaoqiu Huang

in Bioinformatics

Volume 25, issue 8, pages 1082-1083
Published in print April 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp089
PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance

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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@cs.iastate.edu

Supplementary information: Supplementary data are available at Bionformatics online.

Journal Article.  1196 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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