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Abstract
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.
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.
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.