Large Scale Matching for Position Weight Matrices

  • Aude Liefooghe
  • Hélène Touzet
  • Jean-Stéphane Varré
Conference paper

DOI: 10.1007/11780441_36

Volume 4009 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Liefooghe A., Touzet H., Varré JS. (2006) Large Scale Matching for Position Weight Matrices. In: Lewenstein M., Valiente G. (eds) Combinatorial Pattern Matching. CPM 2006. Lecture Notes in Computer Science, vol 4009. Springer, Berlin, Heidelberg

Abstract

This paper addresses the problem of multiple pattern matching for motifs encoded by Position Weight Matrices. We first present an algorithm that uses a multi-index table to preprocess the set of motifs, allowing a dramatically decrease of computation time. We then show how to take benefit from simlar motifs to prevent useless computations.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Aude Liefooghe
    • 1
  • Hélène Touzet
    • 1
  • Jean-Stéphane Varré
    • 1
  1. 1.LIFL – UMR CNRS 8022Villeneuve d’AscqFrance