Self-overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching

Authors:
Aude Liefooghe;Hélène Touzet;Jean-Stéphane Varré
Affiliations:
LIFL - UMR CNRS 8022, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France 59655 and INRIA Lille Nord-Europe, Villeneuve d'Ascq, France 59650;LIFL - UMR CNRS 8022, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France 59655 and INRIA Lille Nord-Europe, Villeneuve d'Ascq, France 59650;LIFL - UMR CNRS 8022, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France 59655 and INRIA Lille Nord-Europe, Villeneuve d'Ascq, France 59650
Venue:
LATA '09 Proceedings of the 3rd International Conference on Language and Automata Theory and Applications
Year:
2009

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Abstract

Position Weight Matrices are broadly used probabilistic motif models. In this paper, we address the problem of identifying and characterizing potential overlaps between occurrences of such a motif. It has useful applications to the statistics of the number of occurrences, and to weighted pattern matching with an extension of the well-known Knuth-Morris-Pratt algorithm.