title: PatternHunter: faster and more sensitive homology search.
abstract: 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.
authors.affiliation: Computer Science Department, University of Western Ontario, London N6A 5B8, Canada Bioinformatics Solutions Inc., 145 Columbia Street West, Waterloo, Ont. N2L 3L2, Canada.
authors.forename: Bin
authors.initials: B
authors.lastname: Ma
authors.forename: John
authors.initials: J
authors.lastname: Tromp
authors.forename: Ming
authors.initials: M
authors.lastname: Li
mesh_terms: 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
chemical_list: D004247:DNA