r2dt-bio/R2DT

Handle fragments better

Opened this issue · 2 comments

blakesweeney commented

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 have internal pairing which leads to things with weird gaps and the like. A better way of dealing with this would be to draw the bits with internal structure correctly and then treat the leading/trailing unstructured regions as large inserted loops. Some examples of problems are:

https://test.rnacentral.org/rna/URS000030CACB/416422
https://test.rnacentral.org/rna/URS0000503191/686583
https://test.rnacentral.org/rna/URS00003ACF95/878000

davidhoksza commented

Is this still relevant, @blakesweeney? The links do not work anymore.