How To Manage Overlaping Features Using Biopython Genomediagram

Question

[dustar1986]

Hi,

I am using Biopython GenomeDiagram to create visual genome features. I read the user guide and found all the example only demonstrate the drawing the non-overlapping features. How can I draw overlapping features on the diagram.

For example,

I want to use an arrow to mark a protein-coding gene on the diagram.

And within this gene, there is an intronic miRNA. So I wanna used another shorter arrow to mark it which locates above the arrow that represents the protein-coding gene.

Which parameter and command should I use to tell biopython these two arrows should have different distances to the x-axis?

Hope I've made myself clear.

Thanks a lot.

[Pappu]

Please try circos.

Answer 1

[Peter]

The simplest solutions are a careful choice of ordering (draw the miRNA on top of the protein coding gene and in a different colour) and using multiple tracks (for example one for protein coding genes, and a separate track for tRNA and miRNA, etc).

There is currently no sub-track positioning of features within GenomeDiagram - if you'd be interested in trying to develop this please sign up on the Biopython development mailing list to discuss it.