Recherche d'instances de motifs expressifs avec Logol. Application à la modélisation d'événements de frameshift -1

Catherine Belleannée 1 Olivier Sallou 2 Jacques Nicolas 1
1 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
2 Plateforme bioinformatique GenOuest [Rennes]
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique
Abstract : The current practice of pattern matching tools and the gap that may be observed with the actual modelling needs of people analysing genome structures clearly demonstrates the need for higher level languages to describe and search for these structures in genomic sequences. It appears necessary to offer new tools allowing to build more expressive models of families of biological sequences, on the basis of their content and structure. This article presents Logol, a new application designed to achieve pattern matching in possibly large sequences with realistic biological motifs. Logol consists in both a language for describing patterns, and the associated parser for effectively scanning sequences (RNA, DNA or protein) with such motifs. The language, based on an high level gramatical formalism, allows to express flexible patterns (with misparings and indels) composed of both sequential and structural elements (such as repeats or pseudoknots). A web page on the GenOuest BioInformatics Platform http://www.genouest.org/ gives access to the Logol application. It includes an interface for graphically drawing the motif model and an interface to display the resulting matches within the targetted pattern. Logol is presented through an illustrative application using a quite intricate motif model, which is the detection of -1 ribosomal frameshifting events in messenger RNA sequences.
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Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Recherche d'instances de motifs expressifs avec Logol. Application à la modélisation d'événements de frameshift -1. JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.5-14. ⟨hal-00726791⟩

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