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Multiseed Lossless Filtration
January-March 2005 (vol. 2 no. 1)
pp. 51-61
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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Index Terms:
Filtration, string matching, gapped seed, gapped q-gram, local alignment, sequence similarity, seed family, multiple spaced seeds, dynamic programming, EST, oligonucleotide selection.
Citation:
Gregory Kucherov, Laurent Noé, Mikhail Roytberg, "Multiseed Lossless Filtration," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 1, pp. 51-61, Jan.-March 2005, doi:10.1109/TCBB.2005.12
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