PatternHunter: faster and more sensitive homology search.

by: B Ma, J Tromp, M Li

Bioinformatics, Vol. 18, No. 3. (March 2002), pp. 440-445.

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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.

@article{citeulike:332260, 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.}, address = {Computer Science Department, University of Western Ontario, London N6A 5B8, Canada Bioinformatics Solutions Inc., 145 Columbia Street West, Waterloo, Ont. N2L 3L2, Canada.}, author = {Ma, B. and Tromp, J. and Li, M. }, citeulike-article-id = {332260}, doi = {http://dx.doi.org/10.1093/bioinformatics/18.3.440}, issn = {1367-4803}, journal = {Bioinformatics}, month = {March}, number = {3}, pages = {440--445}, posted-at = {2008-04-08 09:14:07}, priority = {0}, title = {PatternHunter: faster and more sensitive homology search.}, url = {http://dx.doi.org/10.1093/bioinformatics/18.3.440}, volume = {18}, year = {2002} }

RIS record

TY - JOUR ID - citeulike:332260 L3 - citeulike-article-id:332260 TI - PatternHunter: faster and more sensitive homology search. JF - Bioinformatics VL - 18 IS - 3 SP - 440 EP - 445 AD - Computer Science Department, University of Western Ontario, London N6A 5B8, Canada Bioinformatics Solutions Inc., 145 Columbia Street West, Waterloo, Ont. N2L 3L2, Canada. SN - 1367-4803 N2 - 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. AU - Ma, B AU - Tromp, J AU - Li, M PY - 2002/03// UR - http://dx.doi.org/10.1093/bioinformatics/18.3.440 ER -

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