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Towards structural models for the Ebola UTR regions using experimental SHAPE probing data

Afaf Saaidi 1, 2 Delphine Allouche 3 Bruno Sargueil 3 Yann Ponty 1, 2
1 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
2 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
3 LCRB - UMR 8015 - Laboratoire de cristallographie et RMN biologiques
Abstract : Next-Generation Sequencing (NGS) technologies have opened new perspectives to refine the process of predicting the secondary structure(s) of structured non-coding RNAs. Herein, we describe an integrated modeling strategy, based on the SHAPE chemistry, to infer structural insight from deep se-quencing data. Our approach is based on a pseudo-energy minimization, incorporating additional information from evolutionary data (compensatory mutations) and SHAPE experiments (reactivity scores) within an iterative procedure. Preliminary results reveal conserved and stable structures within UTRs of the Ebola Genome, that are both thermodynamically-stable and highly supported by SHAPE accessibility analysis.
Keywords : High-throughput sequenc- SHAPE chemistry Ebola secondary structure prediction RNA
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Submitted on : Wednesday, June 15, 2016 - 8:49:42 PM
Last modification on : Wednesday, December 15, 2021 - 9:58:33 AM

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CNRS | X | LIX | UNIV-PARIS5 | INRIA | X-LIX | USPC | X-DEP-INFO | UNIV-PARIS | GS-COMPUTER-SCIENCE | INC-CNRS

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Afaf Saaidi, Delphine Allouche, Bruno Sargueil, Yann Ponty. Towards structural models for the Ebola UTR regions using experimental SHAPE probing data. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France. ⟨hal-01332469⟩

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