Skip to Main content Skip to Navigation
Book sections

Introduction to RNA secondary structure comparison.

Stefanie Schirmer 1 Yann Ponty 2, 3, 4 Robert Giegerich 5
1 IRIC - Institut de Recherche en Immunologie et en Cancérologie [UdeM-Montréal]
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
3 SFU - Department of Mathematics [Burnaby]
4 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
5 Universität Bielefeld = Bielefeld University
Abstract : Many methods have been proposed for RNA secondary structure comparison, and new ones are still being developed. In this chapter, we first consider structure representations and discuss their suitability for structure comparison. Then, we take a look at the more commonly used methods, restricting ourselves to structures without pseudo-knots. For comparing structures of the same sequence, we study base pair distances. For structures of different sequences (and of different length), we study variants of the tree edit model. We name some of the available tools and give pointers to the literature. We end with a short review on comparing structures with pseudo-knots as an unsolved problem and topic of active research.
Document type :
Book sections
Complete list of metadata
https://hal.inria.fr/hal-00846818
Contributor : Yann Ponty Connect in order to contact the contributor
Submitted on : Sunday, July 21, 2013 - 11:13:16 AM
Last modification on : Thursday, July 8, 2021 - 3:49:26 AM

Identifiers

Collections

CNRS | INRIA | LIX | X | X-LIX | X-DEP-INFO

Citation

Stefanie Schirmer, Yann Ponty, Robert Giegerich. Introduction to RNA secondary structure comparison.. Gorodkin, Jan and Ruzzo, Walter L. RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods, 1097, Springer, pp.247-73, 2013, Methods in molecular biology, ISBN 978-1-62703-708-2. ⟨10.1007/978-1-62703-709-9_12⟩. ⟨hal-00846818⟩

Export

BibTeX TEI DC DCterms EndNote

Share

Metrics

Les métriques sont temporairement indisponibles

 

Contact                    Legal Notice                    Personal Data