R2DT
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RNAcentral
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
I've come across a bit of an edge case where the naming of the tempfile by tRNAscan-SE is suboptimal, leading to jobs hanging waiting for user input. I'm running the...
Is there a way to export secondary figures with the pseudoknots visible? The MD file makes it sound like removing the pseudoknots is optional?
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...
We are looking at the metadata file for CRW now (https://github.com/RNAcentral/R2DT/blob/master/data/crw-metadata.tsv) and it would be helpful if the models had more precise terms. Specifically there are several models labeled mt_rRNA....
I've noticed some segfaults when running our pipeline which result in errors later when r2dt tries to find an svg that wasn't created. I'm running a singularity container (converted from...
URS000075D341_9606 and URS00021ED94B_9606 are both human 5.8S rRNA sequences that differ only by a single nt (the first is 1nt longer than the second) but their secondary structure diagrams look...
We can detect if the SVG has dashed lines to know if constrained folding was used or not, but still we wouldn't know the fold type. To know all the...
By default, long sequences of regions with unknown are not displayed in Traveler's output. Instead, those are truncated and replaced by x-symbols. I would like to see an option to...
- 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...
It would be very helpful for integration with other data sources if all nucleotides in the svg output of R2DT included a `data-sequence-index` (and something similar in the JSON format)...
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Visualise RNA secondary structure in consistent, reproducible and recognisable layouts