PatternHunter: faster and more sensitive homology search.
BACKGROUND
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.


BACKGROUND
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.
Ma
Bin
B
Computer Science Department, University of Western Ontario, London N6A 5B8, Canada Bioinformatics Solutions Inc., 145 Columbia Street West, Waterloo, Ont. N2L 3L2, Canada.
Tromp
John
J
Li
Ming
M
D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D030561:Databases, Nucleic Acid; D016678:Genome; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009317:National Library of Medicine (U.S.); D011786:Quality Control; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D017385:Sequence Homology; D012984:Software; D013997:Time Factors; D014481:United States
D004247:DNA