Secondary structure

RNAcentral generates secondary structure (2D) diagrams using the R2DT software that visualises RNA structure using standard layouts or templates. Learn more about the method in the R2DT paper or check out the code on GitHub.

R2DT overview

RNAcentral stores RNA secondary structures computed using R2DT for millions of non-coding RNAs. The structures are displayed using a library of ~4,000 templates, including:

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

For each sequence the R2DT pipeline automatically selects the template using ribovore, folds the sequence into the template structure using Infernal, and visualises it using Traveler.

RNA secondary structure in RNAcentral

The secondary structures are displayed in text search results, on RNA sequence pages, and in sequence similarity search results. For example, text search results include simplified outlines of the structures:

Clicking on any thumbnail shows a detailed diagram, such as the following fly RNAse P structure:

What do colours mean?

The differences between the template and the sequence are highlighted in colour. The nucleotides shown in black are identical to the template while the nucleotides that differ from the template are shown in several colours depending on whether it's an insertion (magenta) or modification (green).

R2DT web application

A secondary structure can be generated for an RNA sequence using the R2DT web application.

Template selection

By default R2DT chooses a template automatically but it is possible to choose a template manually by clicking Show advanced and browsing the templates. This option could be useful to highlight species-specific regions. For example, one could display the human small SSU rRNA using a bacterial template.

Constrained folding

The advanced options also enable constrained folding, which uses RNAfold from the Vienna RNA package to add base pairs for the single-stranded regions that are not modelled by the templates. For example, this method can improve microRNA diagrams where the Rfam consensus structure has long dangling ends or large hairpin loops. It can also fold species-specific insertions found in many rRNAs:

There are four ways of using constrained folding:

  • Auto: by default the best mode is chosen automatically based on RNA type and insertion size;
  • Full molecule: the entire molecule is folded using RNAfold with the template structure provided as a constraint;
  • Insertions only: the secondary structure of the insertion relative to the template is predicted with RNAfold and added to the diagram;
  • All constraints enforced: same as above except for the nucleotides that align to single-stranded regions of the template are kept unpaired when predicting the new structure using RNAfold

To use constrained folding, choose one of the modes in the advanced options:

Embeddable widget

It is possible to embed an R2DT secondary structure into any website, and it has already been added to FlyBase, SGD, and Nucleic Acid Knowledgebase.

Find out more about how to integrate this widget into your website.

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