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Bioinformatics. 2007 Nov 15;23(22):2969-77. Epub 2007 Sep 5.

Multiple spaced seeds for homology search.

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  • 1Department of Computer Science, University of Western Ontario, N6A 5B7, London, Ontario, Canada.



Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. The introduction of optimal spaced seeds in PatternHunter has increased both the sensitivity and the speed of homology search, and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, Smith-Waterman sensitivity is approached at BLASTn speed. However, computing optimal multiple spaced seeds was proved to be NP-hard and current heuristic algorithms are all very slow (exponential).


We give a simple algorithm which computes good multiple seeds in polynomial time. Due to a completely different approach, the difference with respect to the previous methods is dramatic. The multiple spaced seed of PatternHunterII, with 16 weight 11 seeds, was computed in 12 days. It takes us 17 s to find a better one. Our approach changes the way of looking at multiple spaced seeds.

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