Large scale matching for position weight matrices

Authors:
Aude Liefooghe;Hélène Touzet;Jean-Stéphane Varré
Affiliations:
LIFL – UMR CNRS 8022, Villeneuve d'Ascq, France;LIFL – UMR CNRS 8022, Villeneuve d'Ascq, France;LIFL – UMR CNRS 8022, Villeneuve d'Ascq, France
Venue:
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Year:
2006

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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.