R2DT
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RNAcentral
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
Seems like in the `generate_traveler_fasta` function (linked below) that there's a possible off-by-one error in generated dot-bracket structures when a sequence contains a leading 5' label. https://github.com/RNAcentral/R2DT/blob/main/utils/rna2djsonschema.py The first for...
Currently R2DT uses the predicted tRNA isotype from tRNAscan-SE to select the corresponding template for Traveler 2D image generation. However, mt-tRNA-Cys in armadillo and some reptides do not have the...
Reduce the number of spawned processes and use Python API instead for tasks like deleting files, unzipping, or wget.
The ribovore team is working on a prototype.
- [x] Make sure all tests pass - [x] Upload precomputed library to the EBI FTP - [x] Update version info in Readme and shared.py - [x] Merge pull request...
It would be useful to establish an integration with [RNAFramework](https://github.com/dincarnato/RNAFramework) so that R2DT can be used to display the secondary structure and reactivities produced by RNAFramework. R2DT should read RNAFramework's...
Hi! First of all, thank you so much for building this tool. The layouts look awesome! I'm developing a python package to analyze and explore RNA structure data in Jupyter...
As pointed out by @pzhaojohnson the model name is not propagated to the json schema output file but it should, and there is a [corresponding field](https://github.com/LDWLab/RNA2D-data-schema/blob/main/example.JSON#L4) in the RNA 2D...
We've been doing a rescan of all sequences in RNAcentral using the latest R2DT, during which it became apparent that we have entries for models that no longer appear in...
Instead of creating tRNA alignments with cmalign and tRNA covariance models, the alignments generated by tRNAscan-SE in the secondary structure output can be used. The alignments generated by tRNAscan-SE use...
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Visualise RNA secondary structure in consistent, reproducible and recognisable layouts