Four types of secondary structure templates are used:
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.
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):
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.