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Introduction to RNA Secondary Structure Comparison

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Book cover RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1097))

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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Acknowledgment

Thanks go to Dr. Ralph Kandalla for a careful endodontic therapy of the first author, see also Fig. 15. Without his expertise, this chapter would not have been completed in time. Thanks also go to Sonja Klingberg for a careful reading of the manuscript.

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Authors and Affiliations

  1. Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Universite de Montre al, Montre al, QC, Canada

    Stefanie Schirmer

  2. CNRS, Laboratoire d’Informatique de l’X (LIX) UMR 7161, INRIA AMIB, Ecole Polytechnique, Palaiseau, France

    Yann Ponty

  3. Faculty of Technology and Center of Biotechnology, Bielefeld University, Bielefeld, Germany

    Robert Giegerich

Authors
  1. Stefanie Schirmer
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  2. Yann Ponty
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  3. Robert Giegerich
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Editor information

Editors and Affiliations

  1. Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

    Jan Gorodkin

  2. University of Washington Dept. Computer Science & Engineering, Seattle, Washington, USA

    Walter L. Ruzzo

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Schirmer, S., Ponty, Y., Giegerich, R. (2014). Introduction to RNA Secondary Structure Comparison. In: Gorodkin, J., Ruzzo, W. (eds) RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Methods in Molecular Biology, vol 1097. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-709-9_12

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  • DOI: https://doi.org/10.1007/978-1-62703-709-9_12

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-708-2

  • Online ISBN: 978-1-62703-709-9

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