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RNAcentral / R2DT

Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
https://r2dt.bio
Apache License 2.0
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Integrate with RiboDraw #59

Open AntonPetrov opened 2 years ago

AntonPetrov commented 2 years ago

R2DT should be able to use diagrams produced by RiboDraw as templates, similar to how it's done with XRNA-GT. This would enable a source of curated diagrams for RNAs with experimentally determined 3D structures. Looks like lots of people would find this useful.

It would be interesting to explore producing multiple diagrams for the same sequence. For example, an rRNA sequence can be visualised using CRW, RiboVision, or RiboDraw layouts.

CC @everyday847 @aspetr01

everyday847 commented 2 years ago

Another way to approach this -- I don't know which is easier? -- is to make RiboDraw output a data format that meets the R2DT spec for a template. Since RiboDraw drawings are graphical objects (i.e., pngs and svgs) it might be harder to engineer the relevant facilities into R2DT than simply to have RiboDraw output something more useful. What does your template spec look like?

aspetr01 commented 2 years ago

If this is the direction to go, I propose to solve a deeper issue first and to develop the WL notation for xrna format. We would need it soon anyway. Currently only a standard base pairing is supported http://rna.ucsc.edu/rnacenter/xrna/xrna_download.html Once it is done, the extended xrna format can be used for portability. Thoughts?

everyday847 commented 2 years ago

Yeah, routing through this sort of XML format is probably reasonable. And it's easy enough to encode edge, edge, orientation as [WHS][WHS][CT] (for example, if you're in the mood for a regex).

The one kind of feature that I personally like a lot about RiboDraw output -- that I don't think is likely supported in xrna format -- is that the linkers for tertiary contacts can be routed around different structural elements so they don't clash. Maybe this is pointless for the purpose of templates (because if there's any significant perturbation, they'll clash and just have to be re-edited) but I think it could be useful, especially if your RNA is large and only deviates in one domain.

AntonPetrov commented 2 years ago

Having RiboDraw output some files that can be used to create R2DT templates is a great idea. Currently we use FASTA/BPSEQ and Traveler files to generate templates and the corresponding covariance models, so that would be the easiest place to start.

I also agree with the xrna or xrna-like format being a good way to go. However, it does feel a bit old school. I guess these days one would use JSON schema or something like that?

The tertiary contact linkers are currently not supported in Traveler (as far as I know), so R2DT templates don't have them. It is a useful feature, maybe @davidhoksza would be interested in implementing it.