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Published Online: 5 July 2004

Occurrence Probability of Structured Motifs in Random Sequences

Publication: Journal of Computational Biology
Volume 9, Issue Number 6

Abstract

The problem of extracting from a set of nucleic acid sequences motifs which may have biological function is more and more important. In this paper, we are interested in particular motifs that may be implicated in the transcription process. These motifs, called structured motifs, are composed of two ordered parts separated by a variable distance and allowing for substitutions. In order to assess their statistical significance, we propose approximations of the probability of occurrences of such a structured motif in a given sequence. An application of our method to evaluate candidate promoters in E. coli and B. subtilis is presented. Simulations show the goodness of the approximations.

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cover image Journal of Computational Biology
Journal of Computational Biology
Volume 9Issue Number 6December 2002
Pages: 761 - 773
PubMed: 12614545

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Published online: 5 July 2004
Published in print: December 2002

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S. Robin
INA-PG / INRA, UMR Biométrie et Intelligence Artificielle, 16, rue Claude Bernard, F-75005 Paris, France;INRA, Unité Mathématique, Informatique and Génome, F-78026 Versailles Cedex, France
J.-J. Daudin
INA-PG / INRA, UMR Biométrie et Intelligence Artificielle, 16, rue Claude Bernard, F-75005 Paris, France
H. Richard
CNRS-UPRESA 8071, Laboratoire Statistique et Génomes, 523, place des Terrasses de l'Agora, Tour Evry 2, F-9100 Évry, France
M.-F. Sagot
INRIA Rhônes-Alpes, Laboratoire de Biométrie Évolutive, University Claude Bernard, 43 bd du 11 novembre 16918, F-69622, Villeurbanes cedex, France
S. Schbath
INRA, Unité Mathématique, Informatique and Génome, F-78026 Versailles Cedex, France

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