title: Patternhunter II: highly sensitive and fast homology search.
abstract: Extending the single optimized spaced seed of PatternHunter(20) to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search methodology research back to a full circle.
authors.affiliation: Department of Computer Science, University of Waterloo, Waterloo, ON, Canada N2L 3G. mli@uwaterloo.ca
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Bin
authors.initials: B
authors.lastname: Ma
authors.forename: Derek
authors.initials: D
authors.lastname: Kisman
authors.forename: John
authors.initials: J
authors.lastname: Tromp
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D030541:Databases, Genetic; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*