Multi-seed Lossless Filtration
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- Kucherov G., Noé L., Roytberg M. (2004) Multi-seed Lossless Filtration. In: Sahinalp S.C., Muthukrishnan S., Dogrusoz U. (eds) Combinatorial Pattern Matching. CPM 2004. Lecture Notes in Computer Science, vol 3109. Springer, Berlin, Heidelberg
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 . 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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