How can I add KEGG functional categories to whole genome alignments?

Question

[Ssri]

Hi! I am looking for packages/servers that can add KEGG gene functional categories to whole genome alignments done on ACT. A reference I am trying to emulate is in panel A here - https://www.nature.com/articles/nature06244/figures/2. How can I overlay this functional information onto genome alignments as shown in the linked figure? Thank you!

Answer 1

[Patrick]

Hi,

do you want to reproduce the figure or want to get the annotation in your genome alignment viewing tool?

The figure you linked does not show a genome alignment, it's just a stacked pie-chart. And while the figure does look nice, there are multiple reasons why you should not use a pie chart for this data! But to reproduce it, a genome alignment is not even required. You only need the annotation for each of your genomes.

For this you might use the KEGG annotation service, either directly on their webpage (if you have only few number of sequences), via API (for selected userbase only iirc) or use their tool locally with the KofamKOALA database as described in this Paper#

Alternatively the eggNOG-mapper also provides transfered KEGG-annotation. In their webservice you can even upload genomic sequences.

I don't exactly know how the outputs looks like, but some further steps might be required to format the output to propper GFF, so you can import it into your viewing tool.

[Ssri]

This sounds like an excellent workflow - thank you! So it seems that if I am able to convert the gene "codes" to functional annotations from KEGG and convert it to GFF, I should be good. Thank you!