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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 positionspecific substitution matrix for the query sequence during the search. The obvious advantage of the approach isdoi:10.1093/bioinformatics/btp089 pmid:19251771 fatcat:pcrm3vingzahdlsmul4f53rg3a