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Journal articles
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.
Cited literature [28 references]
https://hal.archives-ouvertes.fr/hal-00506348
Contributor : Stephanie Beaunay Connect in order to contact the contributor
Submitted on : Monday, November 21, 2011 - 3:15:28 PM
Last modification on : Tuesday, October 19, 2021 - 11:25:51 AM
Long-term archiving on: : Wednesday, February 22, 2012 - 2:20:34 AM
Contributor : Stephanie Beaunay Connect in order to contact the contributor
Submitted on : Monday, November 21, 2011 - 3:15:28 PM
Last modification on : Tuesday, October 19, 2021 - 11:25:51 AM
Long-term archiving on: : Wednesday, February 22, 2012 - 2:20:34 AM
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