Patternhunter II: highly sensitive and fast homology search.
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.
Li
Ming
M
Department of Computer Science, University of Waterloo, Waterloo, ON, Canada N2L 3G. mli@uwaterloo.ca
Ma
Bin
B
Kisman
Derek
D
Tromp
John
J
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*