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RNA Bioinformatics pp 63–100Cite as

Drawing and Editing the Secondary Structure(s) of RNA

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1269))

Abstract

Secondary structure diagrams are essential, in RNA biology, to communicate functional hypotheses and summarize structural data, and communicate them visually as drafts or finalized publication-ready figures. While many tools are currently available to automate the production of such diagrams, their capacities are usually partial, making it hard for a user to decide which to use in a given context. In this chapter, we guide the reader through the steps involved in the production of expressive publication-quality illustrations featuring the RNA secondary structure. We present major existing representations and layouts, and give precise instructions to produce them using available free software, including jViz.RNA, the PseudoViewer, RILogo, R-chie, RNAplot, R2R, and VARNA. We describe the file formats and structural descriptions accepted by popular RNA visualization tools. We also provide command lines and Python scripts to ease the user’s access to advanced features. Finally, we discuss and illustrate alternative approaches to visualize the secondary structure in the presence of probing data, pseudoknots, RNA–RNA interactions, and comparative data.

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Acknowledgements

The author wishes to thank the French Centre National de la Recherche Scientifique (CNRS) for its continued support, the NSF-funded RNA Ontology Consortium, and Jim Procter for stimulating discussions.

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Authors and Affiliations

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

    Yann Ponty

  2. Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, Orsay, France

    Fabrice Leclerc

Authors
  1. Yann Ponty
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  2. Fabrice Leclerc
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Correspondence to Yann Ponty .

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Editors and Affiliations

  1. Department of Biosciences, Biotechnology and Biopharmaceutics, and National Research Council, University of Bari; Institute of Biomembranes and Bioenergetics, Bari, Italy, and National Institute of Biostructures and Biosystems (INBB), Rome, Italy

    Ernesto Picardi

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Ponty, Y., Leclerc, F. (2015). Drawing and Editing the Secondary Structure(s) of RNA. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 1269. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2291-8_5

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  • DOI: https://doi.org/10.1007/978-1-4939-2291-8_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2290-1

  • Online ISBN: 978-1-4939-2291-8

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