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
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.