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 K\"arkk\"ainen [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.
@article{arxiv.0901.3215,
title = {Multiseed Lossless Filtration},
author = {Gregory Kucherov and Laurent Noé and Mikhail A. Roytberg},
journal= {arXiv preprint arXiv:0901.3215},
year = {2011}
}