Alignments of RNA Structures

— We describe a theoretical unifying framework to express comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences, and encompasses 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 evolutionary operations, such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia that is available at the web server http://bioinfo.lifl.fr/RNA/gardenia.

• Type: Journal
• Year: 2010
• Where: TCBB
• Authors: Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet
• Keywords: Arc-annotated Sequences, Polynomial Time Algorithm, Rna Structure, TCBB 2010