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R2DT documentation

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What is R2DT?

The R2DT software automatically generates RNA secondary structure diagrams in consistent, reproducible and recognisable layouts using a library of templates representing a wide range of RNAs.

Try it now

<script type="text/javascript" src="https://rnacentral.github.io/r2dt-web/dist/r2dt-web.js"></script>

How does it work?

Find out more about R2DT, read the R2DT paper, or check out the overview slides:

<iframe src="https://docs.google.com/presentation/d/1DI-_3ozYsGhe21ZUyMeUKn9NrAxjTaoXJ2DF8IPi3Wo/embed?start=false&loop=false&delayms=3000" frameborder="0" width="640" height="389" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true"></iframe>

Examples

The following example visualisations show LSU, SSU, and 5S rRNA, four tRNAs, two RNAse P, snoRNA, MoCo riboswitch, and U4 snRNA:

Examples

Getting started

R2DT can be used in a number of ways:

Who uses R2DT?

  • RNAcentral uses R2DT to visualise >20 million RNA secondary structures
  • PDBe uses R2DT to enable interactive navigation between sequence, 2D and 3D structure (for example, 1S72)
  • Rfam and GtRNAdb display R2DT diagrams in sequence similarity search
  • FlyBase, SGD, and PomBase show R2DT diagrams for RNA genes
  • NAKB uses R2DT to visualise secondary structure of RNAs from PDB (for example, 1S72)
  • RiboVision 2.0 uses R2DT to visualise RNA secondary structure and connect them to multiple sequence alignments and 3D structures

Browse papers citing R2DT →

Citation

If you use R2DT in your work, please consider citing the following paper:

R2DT is a framework for predicting and visualising RNA secondary structure using templates Nature Communications

License

R2DT is available under the Apache 2.0 license.

Get in touch

If you have any questions or feedback, feel free to submit a GitHub issue or contact the RNAcentral help desk.

.. toctree::
   :caption: About R2DT
   :name: about_r2dt
   :maxdepth: 1
   :hidden:

   self
   about

.. toctree::
   :caption: Getting started
   :name: getting_started
   :hidden:
   :maxdepth: 1

   installation
   usage
   annotations
   editors
   api
   widget

.. toctree::
   :caption: Updating R2DT
   :name: updating_r2dt
   :hidden:
   :maxdepth: 1

   templates
   docs
   testing
   docker
   releases

.. toctree::
   :caption: Project info
   :name: project_info
   :hidden:
   :maxdepth: 1

   team
   blog

GitHub

Contribute to the R2DT project on GitHub →