Drawing and Editing the Secondary Structure(s) of RNA. - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Book Sections Year : 2015

Drawing and Editing the Secondary Structure(s) of RNA.

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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RNASecondaryStructureVisualisationChapter.pdf (2.35 Mo) Télécharger le fichier
SupplementaryMaterial.pdf (238.15 Ko) Télécharger le fichier
figs/figure-01-formats.pdf (62.48 Ko) Télécharger le fichier
figs/figure-02-FileFormatExamplesSTOCKHOLM.pdf (142.91 Ko) Télécharger le fichier
figs/figure-03-FileFormatExamplesDBN.pdf (28.61 Ko) Télécharger le fichier
figs/figure-04-FileFormatExamplesPseudoBase.pdf (30.96 Ko) Télécharger le fichier
figs/figure-05-FileFormatExamplesBPSEQ.pdf (95.97 Ko) Télécharger le fichier
figs/figure-06-FileFormatExamplesCT.pdf (50.66 Ko) Télécharger le fichier
figs/figure-07-FileFormatExamplesPDB.pdf (70.79 Ko) Télécharger le fichier
figs/figure-09-workflow-vis.pdf (81.91 Ko) Télécharger le fichier
figs/figure-10-linear-purine-riboswitch.pdf (21.59 Ko) Télécharger le fichier
figs/figure-11-circular-example.pdf (84.42 Ko) Télécharger le fichier
figs/figure-12-RF00059-global.pdf (98.48 Ko) Télécharger le fichier
figs/figure-13-1tn2-full-figure.pdf (47.94 Ko) Télécharger le fichier
figs/figure-14-RF00065_motif_chemprobe.pdf (421.12 Ko) Télécharger le fichier
figs/figure-15-pseudoknots.pdf (91.15 Ko) Télécharger le fichier
figs/figure-16-RF00065_interactions.pdf (35.91 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
Origin : Files produced by the author(s)
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Dates and versions

hal-01079893 , version 1 (31-03-2015)

Identifiers

Cite

Yann Ponty, Fabrice Leclerc. Drawing and Editing the Secondary Structure(s) of RNA.. Ernesto Picardi. RNA Bioinformatics, 1269, Springer New York, pp.63-100, 2015, Methods in Molecular Biology, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_5⟩. ⟨hal-01079893⟩
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