Question: Biopython chromosome drawing with coloring
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gravatar for yh362
6 days ago by
yh3620
yh3620 wrote:

Hi, I am using Bio.graphics.BasicChromosome module. I want to draw a allotetraploid plant genome so that chromosomes coming from different ancestral species have different color coding. I know how to draw the backbone chromosomes but I don't quite get how to fill in colors. Also, for some chromosomes, I need some part of it being one color and the rest being another. Is there a way to do that in this module? What I want is similar to the diagram in the following paper, although I currently don't need those genetic map annotations. Thanks in advance!

https://link.springer.com/article/10.1007%2Fs00122-011-1578-8

biopython • 53 views
ADD COMMENTlink written 6 days ago by yh3620

At a very quick glance here: https://biopython.readthedocs.io/en/latest/Tutorial/chapter_graphics.html#annotated-chromosomes

I think you will basically want to create custom features which correspond to the length of span of each chunk of the ancestral parts, essentially treating them like one really large feature/gene.

This may be a job for something like karyoplotteR instead however.

ADD REPLYlink written 5 days ago by jrj.healey12k

Thanks! I didn't know karyoplotteR before, but it seems promising!

ADD REPLYlink written 5 days ago by yh3620
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