R2DT Version 1.4
We are excited to announce a new release of R2DT. Version 1.4 enables new kinds of visualisations, adds new templates, and brings important technical improvements. Read on to find out more.
Visualising alignment accuracy
R2DT can now visualise additional annotations as data layers on top of the secondary structure diagrams. By default, R2DT displays the expected accuracy of the alignment between the query sequence and the template. The accuracy is calculated by the Infernal software as posterior probabilities.
For example, the following diagram shows the secondary structure of a SAM riboswitch RNA sequence from Bacillus subtilis visualised using the RF00162 Rfam template.
Find out how how to visualise your own data, configure colours, and more.
Pseudoknot visualisation has been one of the most requested features since R2DT’s launch. Starting with version 1.4, R2DT uses templates derived from Rfam families that have pseudoknots annotated in the consensus secondary structure (
SS_cons lines of the Stockholm file format). Upon alignment of a target sequence to the covariance model using Infernal, the pseudoknot annotation is transferred to the alignment using the
cmalign program. The following secondary structure of the Cripavirus IRES includes three pseudoknots:
Starting with version 1.4, it is possible to visualise a sequence and its secondary structure without an existing template using a layout generated by R2R. This functionality is useful as a starting point when generating new templates or in cases when the R2DT template library does not yet have a template for a certain RNA. Find more in the docs.
The documentation has been migrated to the Read The Docs platform and can be found at docs.r2dt.bio.
Ribovore, Traveler, Vienna RNA, R-scape, and other dependencies have been updated.
Automated pre-commit software quality checks have been added.
A new process for testing changes using image similarity instead of file identity has been implemented.
R2DT now runs natively on Apple silicon.
The Docker image size has been reduced 5x.
Teamwork makes the dream work
A big thank you to everyone who helped make this release possible, especially:
Ronny Lorenz for help with Vienna RNA python bindings on Apple silicon,
Last but not least, welcome to a new contributor, Alexey Nayden, who bravely re-engineered the Docker image and developed the new testing setup 👏👏👏
The new software is now available on GitHub and Docker Hub. The RNAcentral web app and the API will be updated with the new software in the coming weeks. Stay tuned for future releases and feel free to let us know if you have any feedback by raising an issue on GitHub.