R2DT
R2DT copied to clipboard
RNAcentral
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
https://rnajournal.cshlp.org/content/27/2/133.full
These might be interesting to use: https://pubmed.ncbi.nlm.nih.gov/17135184/. I think they would have to be redrawn by hand though.
I've been playing a bit with R2DT on RNAcentral and also trying out html embedding. Would it be possible to better center the displayed 2D layout so that it doesn't...
The results file metadata.tsv should record the status of each sequence, even if it crashed or had no 2D.
It can't handle some complex header lines like: ``` >DB|TEXT|MORE Some nice name ``` It seems that having several `|` characters causes esl-sfetch to fail with: ``` Creating SSI index...
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...
Some times fragments of structures (LSU in particular) cover a domain that has a clear internal structure and parts that do not. Currently we try to force the sequence to...
- 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?
Dear @AntonPetrov et al, I am trying to use R2DT to visualize secondary structures of non-coding internal transcribed spacer 2 (ITS2) sequences in a standard layout for evolutionary/phylogenetic analyses (e.g....
R2DT can produce diagrams which are either not visually pleasing or have some issue with the secondary structure. Visually this can mean has a lot of overlaps (https://rnacentral.org/rna/URS000000AD71/1828414), or the...
Metadata
Owner
Metadata
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts