Automated prediction of three-way junction topological families in RNA secondary structures

Alexis Lamiable 1, 2 Dominique Barth 1 Alain Denise 2, 3, 4, * Franck Quessette 1 Sandrine Vial 1 Eric Westhof 5
* Auteur correspondant
3 AMIB - Algorithms and Models for Integrative Biology
CNRS - Centre National de la Recherche Scientifique : UMR8623, X - École polytechnique, Inria Saclay - Ile de France, UP11 - Université Paris-Sud - Paris 11, LRI - Laboratoire de Recherche en Informatique, LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
Abstract : We present an algorithm for automatically predicting the topological family of any RNA three-way junction, given only the information from the secondary structure: the sequence and the Watson-Crick pairings. The parameters of the algorithm have been determined on a data set of 33 three-way junctions whose 3D conformation is known. We applied the algorithm on 53 other junctions and compared the predictions to the real shape of those junctions. We show that the correct answer is selected out of nine possible con gurations 64 % of the time. Additionally, these results are noticeably improved if homology information is used. The resulting software, Cartaj, is available online and downloadable (with source) at: http://cartaj.lri.fr
Type de document :
Article dans une revue
Computational Biology and Chemistry, Elsevier, 2012, 37, pp.1-5. 〈10.1016〉
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https://hal.inria.fr/hal-00641738
Contributeur : Alain Denise <>
Soumis le : mercredi 16 novembre 2011 - 15:17:28
Dernière modification le : vendredi 22 juin 2018 - 13:54:01

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  • HAL Id : hal-00641738, version 1
  • DOI : 10.1016

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Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, et al.. Automated prediction of three-way junction topological families in RNA secondary structures. Computational Biology and Chemistry, Elsevier, 2012, 37, pp.1-5. 〈10.1016〉. 〈hal-00641738〉

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