R2DT
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RNAcentral
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
- 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...
Some sequences will fail to get drawn and we should have a nicer output in metadata to indicate this. Some possibilities include: - Do not list the sequence id when...
Example: https://github.com/nawrockie/ribovore/blob/master/models/ribo.0p20.modelinfo ribotyper can give you an error if scores for two models in different domains are really close, this indicates that ribotyper and its models can't confidently assign the...
Use `--1blast` ribotyper option to search for templates using NCBI blast instead of Infernal. This method is used for all models except for Rfam.
There are several things to consider: - Bundle Rfam and CRW models into 2 files (`all.cm`) and use cmfetch when individual models are needed - Commit all.cm to git or...
- [ ] Make sure all tests pass - [ ] Generate precomputed library - [ ] Update version info in Readme and shared.py - [ ] Deploy the latest...
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Visualise RNA secondary structure in consistent, reproducible and recognisable layouts