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r2dt-bio / R2DT

Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
https://r2dt.bio
Apache License 2.0
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Use RNArtist instead of R2R to avoid overlaps in Rfam templates #38

Open AntonPetrov opened 3 years ago

AntonPetrov commented 3 years ago

The idea is to run RNArtist on Rfam families, get JSON output, convert it into R2DT templates and then anytime anyone tries to visualise a sequence from that Rfam family, R2DT will draw it in the same layout as the consensus.

RNArtist layouts are superior to R2R because they have fewer overlaps (for example, 18S rRNA can be drawn without any overlaps).

AntonPetrov commented 9 months ago

With latest developments in RNArtist, this should be prioritised and included in R2DT 2.0.

AntonPetrov commented 9 months ago

I started experimenting with RNArtist and here is some info about running it with amazoncorretto and an example script: https://github.com/fjossinet/RNArtistCore/issues/3

AntonPetrov commented 9 months ago

The following issue contains an example of generating a template-ready drawing starting with an Rfam alignment: https://github.com/fjossinet/RNArtistCore/issues/5

AntonPetrov commented 9 months ago

RNArtistCore now generates Traveler XML files - all the pieces are in place now to generate new layouts for Rfam families and to use RNArtist for template-free layouts https://github.com/fjossinet/RNArtistCore/issues/6