Jbrowse: importance of draw-basepair-track.pl

Question

[CikLa]

Hi,

I found a script named draw-basepair-track.pl in JBrowse program. May I know, what is that actually? Why do people want to draw the basepair track, is there any need of it? Just curious to know.

Regards,

CikAlal

Answer 1

[cmdcolin]

It is a fairly old feature, but it still works. The functionality is documented here.

There is also an example file "tests/data/base_pairing/XdecoderStructure.gff" on github that you can test out, see https://github.com/GMOD/jbrowse/tree/master/tests/data/base_pairing

Loading script

bin/prepare-refseqs.pl --fasta tests/data/base_pairing/mahoney.fa
bin/draw-basepair-track.pl --gff tests/data/base_pairing/XdecoderStructure.gff

(must have GD::Image perl installed)

Example base pairing track

[cmdcolin]

note for future generations you might consider the sashimiplot plugin https://github.com/elsiklab/sashimiplot/ it renders arcs in JS instead of pre-rendering to disk with libgd

Answer 2

[Mitch Skinner]

The original motivating application was to show patterns of base pairing in RNA secondary structures.