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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
Published on: May 24, 2017
Alignments of RNA structures
Guillaume Blin1, Alain Denise, Serge Dulucq
1Institut Gaspard Monge, UMR 8049 CNRS, Université Paris-Est, 5 Bd Descartes-Champs sur Marne, 77454 Marne La Vallée Cedex 2, France. gblin@univ-mlv.fr
Abstract:
We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia.
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