R2DT: a comprehensive platform for visualizing RNA secondary structure

  1. Holly McCann
  2. Caeden D Meade
  3. Loren Dean Williams
  4. Anton S Petrov
  5. Philip Z Johnson
  6. Anne E Simon
  7. David Hoksza
  8. Eric P Nawrocki
  9. Patricia P Chan
  10. Todd M Lowe
  11. Carlos Eduardo Ribas
  12. Blake A Sweeney
  13. Fábio Madeira
  14. Stephen Anyango
  15. Sri Devan Appasamy
  16. Mandar Deshpande
  17. Mihaly Varadi
  18. Sameer Velankar
  19. Craig L Zirbel
  20. Aleksei Naiden
  21. Fabrice Jossinet
  22. Anton I Petrov
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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.

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  1. Version published to 10.1093/nar/gkaf032
  2. Version published to 10.1101/2024.09.29.611006 on bioRxiv