PatternHunter: faster and more sensitive homology search

Bioinformatics. 2002 Mar;18(3):440-5. doi: 10.1093/bioinformatics/18.3.440.


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, 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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • DNA / genetics*
  • Databases, Nucleic Acid*
  • Genome
  • Models, Statistical
  • Molecular Sequence Data
  • National Library of Medicine (U.S.)
  • Quality Control
  • Sensitivity and Specificity
  • Sequence Alignment / methods*
  • Sequence Alignment / statistics & numerical data
  • Sequence Homology*
  • Software*
  • Time Factors
  • United States


  • DNA