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Large Scale Matching for Position Weight Matrices

Aude Liefooghe 1, 2 Helene Touzet 1, 2 Jean-Stéphane Varré 1, 2
2 SEQUOIA - Sequential Learning
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
Abstract : This paper addresses the problem of multiple pattern match- ing 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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Contributor : Jean-Stéphane Varré Connect in order to contact the contributor
Submitted on : Friday, April 4, 2008 - 11:37:07 AM
Last modification on : Monday, September 30, 2019 - 3:36:03 PM

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Aude Liefooghe, Helene Touzet, Jean-Stéphane Varré. Large Scale Matching for Position Weight Matrices. Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.401-412, ⟨10.1007/11780441_36⟩. ⟨inria-00270270⟩



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