Combinatorial Pattern Matching

Volume 4009 of the series Lecture Notes in Computer Science pp 401-412

Large Scale Matching for Position Weight Matrices

  • Aude LiefoogheAffiliated withLIFL – UMR CNRS 8022
  • , Hélène TouzetAffiliated withLIFL – UMR CNRS 8022
  • , Jean-Stéphane VarréAffiliated withLIFL – UMR CNRS 8022

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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.