Issue No. 01 - January-March (2005 vol. 2)
DOI Bookmark: http://doi.ieeecomputersociety.org/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 Kärkkäinen . 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.
Filtration, string matching, gapped seed, gapped q-gram, local alignment, sequence similarity, seed family, multiple spaced seeds, dynamic programming, EST, oligonucleotide selection.
L. Noé, G. Kucherov and M. Roytberg, "Multiseed Lossless Filtration," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. , pp. 51-61, 2005.