Multi-seed Lossless Filtration

  • Gregory Kucherov
  • Laurent Noé
  • Mikhail Roytberg
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3109)


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.


Dynamic Programming Algorithm Single Seed Pigeon Hole Principle Seed Family Binary Word 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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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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