Alignments of RNA structures.
IEEE/ACM Trans Comput Biol Bioinform
; 7(2): 309-22, 2010.
Article
em En
| MEDLINE
| ID: mdl-20431150
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.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
RNA
/
Biologia Computacional
/
Modelos Genéticos
Idioma:
En
Ano de publicação:
2010
Tipo de documento:
Article