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.
|Number of pages||14|
|Journal||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Publication status||Published - 2004|