PatternHunter: faster and more sensitive homology search

PatternHunter: faster and more sensitive homology search (2002)

by Bin Ma , John Tromp , Ming Li

Venue:	BIOINFORMATICS
Citations:	201 - 20 self

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Datum	Value	Source
TITLE	PatternHunter: faster and more sensitive homology search	user correction
AUTHOR NAME	Bin Ma	user correction
AUTHOR AFFIL	University of Western Ontario	user correction
AUTHOR ADDR	London N6A 5B8, Canada	user correction
AUTHOR NAME	John Tromp	user correction
AUTHOR AFFIL	Bioinformatics Solutions Inc.	user correction
AUTHOR ADDR	145 Columbia Street West, Waterloo, Ont. N2L 3L2, Canada	user correction
AUTHOR NAME	Ming Li	user correction
AUTHOR AFFIL	Computer Science Department, University of Waterloo	user correction
AUTHOR ADDR	Waterloo, Ont. N2L 3G1	user correction
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	user correction
YEAR	2002	user correction
VENUE	BIOINFORMATICS	user correction
VENUE TYPE	JOURNAL	INFERENCE
PAGES	440--445	user correction
VOLUME	18	user correction
NUMBER	3	user correction
CITATIONS	6 found	ParsCit 1.0