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Bioinformatics Advance Access originally published online on January 25, 2005
Bioinformatics 2005 21(9):2097-2098; doi:10.1093/bioinformatics/bti257
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

TruMatch—a BLAST post-processor that identifies bona fide sequence matches to genome assemblies

Weixi Li 1, Cathryn J. Rehmeyer 2, Chuck Staben 1 and Mark L. Farman 2,*

1Department of Biological Sciences, University of Kentucky Lexington, KY 40546, USA
2Department of Plant Pathology, University of Kentucky Lexington, KY 40546, USA

*To whom correspondence should be addressed.

Summary: BLAST is a widely used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs, HSPs) 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 be easily overlooked. To rectify this problem, we developed TruMatch—a program that parses standard BLAST outputs and identifies HSPs 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.

Availability: TruMatch is written in Perl and is freely available to non-commercial users via web download at the URL: http://genome.kbrin.uky.edu/fungi_tel/TruMatch/

Contact: farman{at}uky.edu


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Home page
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[Abstract] [Full Text] [PDF]


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