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

Yann Ponty; Fabrice Leclerc

doi:10.1007/978-1-4939-2291-8_5

Book Sections Year : 2015

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

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Yann Ponty

Function : Author
PersonId : 3138
IdHAL : yann-ponty
ORCID : 0000-0002-7615-3930
IdRef : 113491611

Laboratoire d'informatique de l'École polytechnique [Palaiseau]

Algorithms and Models for Integrative Biology

Department of Mathematics [Burnaby]

Fabrice Leclerc

Function : Author
PersonId : 5492
IdHAL : fabrice-leclerc
ORCID : 0000-0002-5641-1525
IdRef : 231160992

Institut de génétique et microbiologie [Orsay]

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.

Keywords

Visualization RNA Bioinformatics Secondary Structure Multiple Sequence Alignments Pseudoknots

Domains

Computer Science [cs] Bioinformatics [q-bio.QM]

Fichier principal

RNASecondaryStructureVisualisationChapter.pdf (2.35 Mo)

figs/figure-01-formats.pdf (62.48 Ko)

figs/figure-02-FileFormatExamplesSTOCKHOLM.pdf (142.91 Ko)

figs/figure-03-FileFormatExamplesDBN.pdf (28.61 Ko)

figs/figure-04-FileFormatExamplesPseudoBase.pdf (30.96 Ko)

figs/figure-05-FileFormatExamplesBPSEQ.pdf (95.97 Ko)

figs/figure-06-FileFormatExamplesCT.pdf (50.66 Ko)

figs/figure-07-FileFormatExamplesPDB.pdf (70.79 Ko)

figs/figure-09-workflow-vis.pdf (81.91 Ko)

figs/figure-10-linear-purine-riboswitch.pdf (21.59 Ko)

figs/figure-11-circular-example.pdf (84.42 Ko)

figs/figure-12-RF00059-global.pdf (98.48 Ko)

figs/figure-13-1tn2-full-figure.pdf (47.94 Ko)

figs/figure-14-RF00065_motif_chemprobe.pdf (421.12 Ko)

figs/figure-15-pseudoknots.pdf (91.15 Ko)

figs/figure-16-RF00065_interactions.pdf (35.91 Ko)

SupplementaryMaterial.pdf (238.15 Ko)

Origin : Files produced by the author(s)

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https://hal.inria.fr/hal-01079893

Submitted on : Tuesday, March 31, 2015-4:59:33 PM

Last modification on : Friday, March 24, 2023-2:53:00 PM

Long-term archiving on: Tuesday, April 18, 2017-6:22:30 AM

Dates and versions

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

Identifiers

HAL Id : hal-01079893 , version 1
DOI : 10.1007/978-1-4939-2291-8_5
PUBMED : 25577373

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

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