Homology ­modeling of complex structural RNAs

Wei Wang​ 1 Matthieu Barba​ 2 Philippe Rinaudo​ 1 Alain Denise 2, 1 Yann Ponty 3, 4
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 : Aligning macromolecules such as proteins, DNAs and RNAs in order to reveal, or conversely exploit, their functional homology is a classic challenge in bioinformatics, with far­reaching applications in structure modelling and genome annotations. In the specific context of complex RNAs, featuring pseudoknots, multiple interactions and non­canonical base pairs, multiple algorithmic solutions and tools have been proposed for the structure/sequence alignment problem. However, such tools are seldom used in practice, due in part to their extreme computational demands, and because of their inability to support general types of structures. Recently, a general parameterized algorithm based on tree decomposition of the query structure has been designed by Rinaudo et al. We present an implementation of the algorithm within a tool named LiCoRNA. We compare it against state­of­the­art algorithms. We show that it both gracefully specializes into a practical algorithm for simple classes pseudoknot, and offers a general solution for complex pseudoknots, which are explicitly out­of­reach of competing softwares.
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Wei Wang​, Matthieu Barba​, Philippe Rinaudo​, Alain Denise, Yann Ponty. Homology ­modeling of complex structural RNAs. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France. ⟨hal-01332642⟩

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