How would you define homologous windows between 2 genomes?

Question

[Axzd]

Hello,

Let's say I have genome A and genome B, each of a single chromosome. How would you define homologous windows between the two?

What I can think of is 1) mapping with minimap2 the 2 chromosomes 2) look at the output to find homologous blocks in the paf file.

Does this sound like the correct approach? Now my problem is, what do I do if I want, say, windows of 10 Kb? How do I go from a PAF file to a bed file with 10 Kb windows that are homologous between genomes A and B. Any idea of the tools or approach?

Thanks

[biofalconch]

Depends what you are interested in, you could go by using a genome-genome alignment using Cactus (https://github.com/ComparativeGenomicsToolkit/cactus).

[dthorbur]

SatsumaSynteny may also be of interest, which is a k-mer based genome-genome alignment tool. If you're just looking at regions around genes, you could use an anchored synteny tool. I'm a little out of date with these, but something like MCScanX may be suitable.

[Axzd]

Thanks! I think this will do