Subset Seed Automaton

  • Gregory Kucherov
  • Laurent Noé
  • Mikhail Roytberg
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4783)


We study the pattern matching automaton introduced in [1] for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much smaller than the one obtained by applying the Aho-Corasick construction. We study properties of this automaton and present an efficient implementation of the automaton construction. We also present some experimental results and show that this automaton can be successfully applied to more general situations.


spaced seed subset seed automaton seed sensitivity 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Gregory Kucherov
    • 1
  • Laurent Noé
    • 1
  • Mikhail Roytberg
    • 2
  1. 1.LIFL/CNRS/INRIA, Bât. M3 Cité Scientifique, 59655, Villeneuve d’Ascq cedexFrance
  2. 2.Institute of Mathematical Problems in Biology, Pushchino, Moscow Region, 142290Russia

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