Multiseed Lossless Filtration

Details Multiseed Lossless Filtration Multiseed Lossless Filtration

2009-01-21

arxiv.org/abs/0901.3215v1

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2 (1) : 51-61, 2005

Biology

Quantitative Biology

Quantitative Methods

Scientific paper

10.1109/TCBB.2005.12

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 K\"arkk\"ainen [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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