Multi-seed Lossless Filtration

  • Gregory Kucherov
  • Laurent Noé
  • Mikhail Roytberg
Conference paper

DOI: 10.1007/978-3-540-27801-6_22

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3109)
Cite this paper as:
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

Abstract

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 [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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Gregory Kucherov
    • 1
  • Laurent Noé
    • 1
  • Mikhail Roytberg
    • 2
  1. 1.INRIA/LORIAVillers-lès-NancyFrance
  2. 2.Institute of Mathematical Problems in BiologyPushchino, Moscow RegionRussia

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