Alignments of RNA structures.

Guillaume Blin; Alain Denise; Serge Dulucq; Claire Herrbach; Helene Touzet

doi:10.1109/TCBB.2008.28

Alignments of RNA structures.

Guillaume Blin ^{1, *} Alain Denise ^{2, 3, 4} Serge Dulucq ⁵ Claire Herrbach ³ Helene Touzet ^{6, 7}

* Corresponding author

1 LIGM - Laboratoire d'Informatique Gaspard-Monge

2 LRI - Laboratoire de Recherche en Informatique

3 IGM - Institut de génétique et microbiologie [Orsay]

4 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

5 LaBRI - Laboratoire Bordelais de Recherche en Informatique

6 LIFL - Laboratoire d'Informatique Fondamentale de Lille

7 SEQUOIA - Sequential Learning

LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe

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.

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Biochemistry, Molecular Biology

Computer Science [cs] / Bioinformatics [q-bio.QM]

Life Sciences [q-bio] / Quantitative Methods [q-bio.QM]

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