Large Scale Matching for Position Weight Matrices

Aude Liefooghe (1, 2) , Helene Touzet (1, 2) , Jean-Stéphane Varré (1, 2)

1 LIFL - Laboratoire d'Informatique Fondamentale de Lille
2 SEQUOIA - Sequential Learning

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.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

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⟩