Flexible RNA design under structure and sequence constraints using formal languages

Abstract : The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.
Type de document :
Communication dans un congrès
ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States. 2013
Liste complète des métadonnées

Littérature citée [26 références]  Voir  Masquer  Télécharger

https://hal.inria.fr/hal-00823279
Contributeur : Yann Ponty <>
Soumis le : jeudi 1 août 2013 - 19:22:23
Dernière modification le : mercredi 14 novembre 2018 - 16:08:06
Document(s) archivé(s) le : mercredi 5 avril 2017 - 18:59:13

Fichiers

design.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

  • HAL Id : hal-00823279, version 2
  • ARXIV : 1305.3830

Citation

Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, et al.. Flexible RNA design under structure and sequence constraints using formal languages. ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States. 2013. 〈hal-00823279v2〉

Partager

Métriques

Consultations de la notice

1543

Téléchargements de fichiers

297