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
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 Department of Mathematics [Burnaby]
4 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
5 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.
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https://hal.inria.fr/hal-00846818
Contributor : Yann Ponty <>
Submitted on : Sunday, July 21, 2013 - 11:13:16 AM
Last modification on : Wednesday, April 17, 2019 - 12:15:34 PM

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INRIA | LIX | X-LIX | PARISTECH | X | X-DEP-INFO

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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⟩

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