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Journal Article Ppublish 19 citations

PubMed: 39921562 DOI: 10.1093/nar/gkaf032

R2DT: a comprehensive platform for visualizing RNA secondary structure.

Nucleic Acids Res 53(4)

Authors: Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Anne E Simon, David Hoksza, Eric P Nawrocki, Patricia P Chan, Todd M Lowe, Carlos Eduardo Ribas, Blake A Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, Mandar Deshpande, Mihaly Varadi, Sameer Velankar, Craig L Zirbel, Aleksei Naiden, Fabrice Jossinet, Anton I Petrov

Affiliations

  • NASA Center for Integration of the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, United States.
  • School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0400, United States.
  • Department of Biomedical Data Science, Stanford University, Palo Alto, CA, 94305-5102, United States.
  • Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, United States.
  • Department of Software Engineering, Charles University, Prague 118 00, Czech Republic.
  • National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States.
  • Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, United States.
  • European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.
  • Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, United States.
  • Independent Researcher, Tbilisi, Georgia.
  • Faculty of Life Sciences, University of Strasbourg, Strasbourg 67000, France.
  • Riboscope Ltd, 23 King Street, Cambridge CB1 1AH, United Kingdom.

Abstract

RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.

MeSH

Nucleic Acids, Rna

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