Patternhunter II: highly sensitive and fast homology search

J Bioinform Comput Biol. 2004 Sep;2(3):417-39. doi: 10.1142/s0219720004000661.

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.

Publication types

  • Comparative Study
  • Evaluation Study
  • Validation Study

MeSH terms

  • Algorithms*
  • Artificial Intelligence*
  • Databases, Genetic
  • Pattern Recognition, Automated / methods*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Sequence Analysis / methods*