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Computational Complexity of Word Counting

  • Mireille Régnier
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2066)

Abstract

Evaluation of the frequency of occurrences of a given set of patterns in a DNA sequence has numerous applications and has been extensively studied recently. We discuss the computational complexity for explicit formulae derived by several authors. We introduce a correlation automaton, that minimizes this complexity. This is crucial for practical applications. Notably, it allows to deal with the Markovian probability model. The case of patterns with some unspecified characters - approximate searching, regular expressions,... - is addressed.

Keywords

Computational Complexity Markovian Model Regular Expression Word Counting Pattern Occurrence 
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 2001

Authors and Affiliations

  • Mireille Régnier
    • 1
  1. 1.INRIALe Chesnay

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