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Journal Articles IEEE/ACM Transactions on Computational Biology and Bioinformatics Year : 2010

Alignments of RNA structures.

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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Dates and versions

hal-00506348 , version 1 (21-11-2011)

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Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet. Alignments of RNA structures.. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, 7 (2), pp.309-322. ⟨10.1109/TCBB.2008.28⟩. ⟨hal-00506348⟩
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