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Alignments of RNA Structures

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5 Author(s)
Guillaume Blin ; Inst. Gaspard Monge, Univ. Paris-Est, Marne-la-Vallee, France ; Alain Denise ; Serge Dulucq ; Claire Herrbach
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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.

Published in:

IEEE/ACM Transactions on Computational Biology and Bioinformatics  (Volume:7 ,  Issue: 2 )