Anton Petrov

Infernal-driven mapping does not work in 2 cases: 1) For tRNAs there is a depairing step to remove non-canonical basepairs so that the number of basepairs is different between the...

Integrate with JAR3D

1

- install JAR3D - extract hairpin and internal loops - run the loops through JAR3D - decide on the cutoff for which JAR3D results to display - generate a summary...

Create templates for 5S RNAs with expansion segments

1

https://rnajournal.cshlp.org/content/27/2/133.full

Add FAIL and NO_HIT to metadata.tsv

1

The results file metadata.tsv should record the status of each sequence, even if it crashed or had no 2D.

Integrate with RiboDraw

4

R2DT should be able to use diagrams produced by [RiboDraw](https://github.com/DasLab/RiboDraw) as templates, similar to how it's done with [XRNA-GT](https://github.com/LDWLab/XRNA-GT). This would enable a source of curated diagrams for RNAs with...

Clean up CRW templates

1

- Consider deleting the intron templates - Make sure each organism has only 1 template - Are there any closely related templates where a single representative can be selected?

- construct a test set (could use [tests.py](https://github.com/RNAcentral/R2DT/blob/master/tests/tests.py) as a starting point) - perform timing experiments to see how long each step takes as a way to identify the bottlenecks...

This could be useful for expert users so that instead of tweaking the resulting diagram they can tweak the input alignment.

In one case, `d.5.e.D.melanogaster.2.bpseq`, the sequence was slightly different between the file in `crw-fasta-no-pseudoknots` and the corresponding postscript file. There may be other cases like this that prevent Traveler from...