CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2005 vol.2 Issue No.01 - January-March
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.
Gregory Kucherov, Mikhail Roytberg, "Multiseed Lossless Filtration", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.2, no. 1, pp. 51-61, January-March 2005, doi:10.1109/TCBB.2005.12