Question: Biopython chromosome drawing with coloring
0
gravatar for yh362
11 months ago by
yh36230
yh36230 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 • 270 views
ADD COMMENTlink written 11 months ago by yh36230
1

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 11 months ago by Joe16k

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

ADD REPLYlink written 11 months ago by yh36230
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