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arXiv · 0901.3215

Multiseed Lossless Filtration

Gregory Kucherov·Laurent Noé·Mikhail A. Roytberg
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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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Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg. 2009-01-21. Multiseed Lossless Filtration. https://doi.org/10.1109/tcbb.2005.12

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