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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.
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Li, M., MA, B., Kisman, D., & Tromp, J. (2004). PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH. Journal of Bioinformatics and Computational Biology, 02(03), 417–439. https://doi.org/10.1142/s0219720004000661
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