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
1MCB - McGill Centre for Bioinformatics (4th floor, Bellini Building, Life Sciences Complex ; 3649 Promenade Sir William Osler ; Montréal, Québec - Canada)
McGill University (845, rue Sherbrooke O. Montréal (Québec) Canada H3A 0G4 - Canada)
2McGill University (845, rue Sherbrooke O. Montréal (Québec) Canada H3A 0G4 - Canada)
3AMIB - Algorithms and Models for Integrative Biology (Algorithmes et modèles pour la Biologie Intégrative
Bâtiment Alan Turing - Campus de l'École Polytechnique - 1 rue Honoré d'Estienne d'Orves - 91120 Palaiseau - France)
Abstract : Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional properties of non-coding RNAs. In this paper, we introduce a formal framework to combine the biochemical signal collected from mutate-and-map experiments, with the evolutionary information available in multiple sequence alignments. We apply neutral theory principles to detect complex long-range dependencies between nucleotides of a single stranded RNA, and implement these ideas into a software called aRNhAck. We illustrate the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA-RNA, RNA-protein, RNA-DNA and RNA-ligand interfaces. aRNhAck is freely available at http://csb.cs.mcgill.ca/arnhack.
https://hal.inria.fr/hal-01291754
Contributor : Yann Ponty
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Submitted on : Tuesday, March 22, 2016 - 9:24:21 AM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM
Long-term archiving on : Sunday, November 13, 2016 - 10:07:42 PM
