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Patternhunter II: highly sensitive and fast homology search
Ming Li1, Bin Ma, Derek Kisman
1Department of Computer Science, University of Waterloo, Waterloo, ON, Canada N2L 3G. mli@uwaterloo.ca
Journal of Bioinformatics and Computational Biology
|September 11, 2004
Summary
PatternHunter II enhances homology search by using multiple spaced seeds, achieving high sensitivity comparable to Smith-Waterman at the speed of Blastn.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Homology search is crucial for understanding gene and protein function.
- Existing tools like Blastn offer speed but lack sensitivity.
- Smith-Waterman provides high sensitivity but is computationally slow.
Purpose of the Study:
- To develop a novel homology search tool, PatternHunter II.
- To address the limitations of speed and sensitivity in current homology search methods.
Main Methods:
- PatternHunter II extends the single optimized spaced seed approach to multiple seeds.
- The method optimizes seed selection for improved detection of homologous sequences.
Main Results:
- PatternHunter II achieves sensitivity close to Smith-Waterman.
- The tool operates at speeds comparable to Blastn.
Conclusions:
- PatternHunter II offers a balanced solution for homology search, combining speed and sensitivity.
- This advancement represents a significant step forward in homology search methodology.