Subset Seed Automaton

  • Gregory Kucherov
  • Laurent Noé
  • Mikhail Roytberg
Conference paper

DOI: 10.1007/978-3-540-76336-9_18

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4783)
Cite this paper as:
Kucherov G., Noé L., Roytberg M. (2007) Subset Seed Automaton. In: Holub J., Žďárek J. (eds) Implementation and Application of Automata. CIAA 2007. Lecture Notes in Computer Science, vol 4783. Springer, Berlin, Heidelberg

Abstract

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.

Keywords

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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