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Multiseed Lossless Filtration

Abstract : We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Kärkkäinen [1]. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database.
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Submitted on : Wednesday, January 21, 2009 - 10:40:13 AM
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Gregory Kucherov, Laurent Noé, Mikhail Roytberg. Multiseed Lossless Filtration. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2005, 2 (1), pp.51-61. ⟨10.1109/TCBB.2005.12⟩. ⟨inria-00354810⟩



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