BLAST is a widely-used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs) are assigned a score based on alignment length and quality and, by default, are reported with the top-scoring matches listed first. For certain types of searches, however, this method of reporting is not optimal. This is particularly true when searching a genome sequence with a query that was derived from the same genome, or a closely related one. If the genome is complex and the assembly is far from complete, correct matches are often relegated to low positions in the results, where they may easily be overlooked. To rectify this problem, we developed TruMatch - a program that parses standard BLAST outputs and identifies high-scoring pairs that involve query segments with unique matches to the assembly. Candidates for bona fide matches between a query sequence and a genome assembly are listed at the top of the TruMatch output.
TruMatch -A BLAST post-processor that identifies and reports bona fide sequence matches.
Bioinformatics.2005 Jan 25; [Epub ahead of print] [Link to the paper]
Weixi Li1, Cathryn J. Rehmeyer2, Chuck Staben1 and Mark L. Farman2 (1Department of Biological Sciences and 2Department of Plant Pathology, University of Kentucky).