R2DT (which stands for RNA 2D Templates) is a software package that visualises RNA secondary structure in standard layouts representing a wide range of RNAs:
- 3D-structure based SSU and LSU rRNA from RiboVision
- 5S and SSU rRNA from CRW
- tRNA from GtRNAdb
- RNAse P from Ribonuclease P Database
- RNA families from Rfam
The R2DT pipeline includes the following steps:
-
Generate a library of covariance models using BPSEQ files from CRW, RiboVision or another source with Infernal. For best results, remove pseudoknots from the secondary structures using RemovePseudoknots from the RNAStructure package.
-
Select the best matching covariance model for each input sequence using Ribovore or tRNAScan-SE 2.0.
-
Fold input sequence into a secondary structure compatible with the template using the top scoring covariance model.
-
Generate secondary structure diagrams using Traveler and the secondary structure layouts.
For a detailed method description see the R2DT paper.