Multi-seed Lossless Filtration (Extended Abstract)

Abstract

We study a method of seed-based lossless filtration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Karkkainen [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.

DOI: 10.1007/978-3-540-27801-6_22

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Cite this paper

@inproceedings{Kucherov2004MultiseedLF, title={Multi-seed Lossless Filtration (Extended Abstract)}, author={Gregory Kucherov and Laurent No{\'e} and Mikhail A. Roytberg}, booktitle={CPM}, year={2004} }