|
1
|
McCann H, Meade C, Williams L, Petrov A, Johnson P, Simon A, Hoksza D, Nawrocki E, Chan P, Lowe T, Ribas C, Sweeney B, Madeira F, Anyango S, Appasamy S, Deshpande M, Varadi M, Velankar S, Zirbel C, Naiden A, Jossinet F, Petrov A. R2DT: a comprehensive platform for visualizing RNA secondary structure. Nucleic Acids Res 2025; 53:gkaf032. [PMID: 39921562 PMCID: PMC11806352 DOI: 10.1093/nar/gkaf032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 12/17/2024] [Accepted: 01/14/2025] [Indexed: 02/10/2025] Open
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.
Collapse
Affiliation(s)
- Holly McCann
- 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
| | - Caeden D Meade
- 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
| | - Loren Dean Williams
- 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
| | - Anton S Petrov
- 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
| | - Philip Z Johnson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, United States
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, United States
| | - David Hoksza
- Department of Software Engineering, Charles University, Prague 118 00, Czech Republic
| | - Eric P Nawrocki
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Patricia P Chan
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Carlos Eduardo Ribas
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Blake A Sweeney
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Fábio Madeira
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stephen Anyango
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sri Devan Appasamy
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mandar Deshpande
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mihaly Varadi
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sameer Velankar
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, United States
| | | | - Fabrice Jossinet
- Faculty of Life Sciences, University of Strasbourg, Strasbourg 67000, France
| | - Anton I Petrov
- Riboscope Ltd, 23 King Street, Cambridge CB1 1AH, United Kingdom
| |
Collapse
|