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
* Corresponding author
3 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
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:
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Contributor : Alain Denise <>
Submitted on : Wednesday, November 16, 2011 - 3:17:28 PM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM


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


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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