Secondary structure

RNAcentral generates secondary structure (2D) diagrams using the R2DT software that visualises RNA structure using standard layouts or templates. Learn more in the R2DT paper

2D templates

Four types of secondary structure templates are used:

  1. Small rRNA subunit (SSU) and 5S rRNA templates from the Comparative RNA Website (CRW);
  2. Rfam consensus secondary structures for all other RNA types;
  3. Small and large rRNA subunit (LSU) templates from RiboVision;
  4. Isotype-specific tRNA templates from GtRNAdb.

For each sequence the R2DT pipeline automatically selects the template using a custom set of covariance models, folds the sequence into the template structure using Infernal, and visualises it using Traveler.

Browse all RNAs with secondary structures

What do colours mean?

The differences between the template and the sequence are highlighted in colour. For example, in the following Thermus thermophilus SSU structure nucleotides shown in black are identical to the CRW template while the nucleotides that differ from the template are shown in several colours depending on whether it's an insertion (red) or modification (green):

Acknowledgements

We would like to thank David Hoksza for help with the Traveler software, Robin Gutell for providing the rRNA templates, Eric Nawrocki for help with the ribotyper software, Anton S. Petrov for the LSU templates, as well as Patricia Chan and Todd Lowe for providing the tRNA templates.


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