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Comparative Study
. 2002 Mar;18(3):440-5.
doi: 10.1093/bioinformatics/18.3.440.

PatternHunter: faster and more sensitive homology search

Bin Ma  1 , John Tromp, Ming Li
Affiliations
Comparative Study

PatternHunter: faster and more sensitive homology search

Bin Ma et al. Bioinformatics. 2002 Mar.

Abstract

Motivation: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation.

Results: We present a new homology search algorithm 'PatternHunter' that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop.

Availability: PatternHunter is available at http://www.bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free.

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