Visualization of DNA-level Collinearity Using Mummer Data

[saltyduckegg]

Hello,

I’ve been admiring the chromosome collinearity images produced by the jcvi.graphics.karyotype module; they are indeed very beautiful. However, it seems that this module is designed primarily to display gene-based collinearity. I have generated similar DNA-level collinearity information using Mummer and am wondering if there is an existing method to visualize such data.

Technically, creating a visualization for DNA-level collinearity should be simpler than for gene-level, but I haven’t been able to find any tutorials or guides on this. Here is an example of the DNA-level collinearity data I have:

38086833 38093476  | 34191579 34198229  |     6644     6651  |    95.72  |     0.00     0.00  | Chr4    Chr6
38100428 38108499  | 34217030 34225121  |     8072     8092  |    98.42  |     0.00     0.00  | Chr4    Chr6
... (additional data) ...
41812689 41877688  | 38158770 38223769  |    65000    65000  |   100.00  |     0.02     0.02  | Chr4    Chr6

Does anyone know of tools or methods that can utilize this type of data for visualization purposes? Any pointers or references would be greatly appreciated.

Thank you!

[saltyduckegg]

I wanna to build this fig, but based in DNA-level.
If there are no methods available, I might have to resort to converting these correspondences into fake gene IDs and BED files for plotting. This is not an good solution.

[Adamtaranto]

There is an experimental version of the micro synteny plotting module that allows for plotting alignment blocks from whole chromosome alignments distinct from the gene annotations.I haven’t implemented this for the macrosynteny plots i.e. with multiple chromosomes per genome.