Use OrthoDB to retrieve the orthologs between human and bacteria

Question

[wangdp123]

Hi there,

I am investigating the data from OrthoDB and trying to find out if the data include the orthologs between human and bacteria.

At the first glance, it seems it doesn't have such kind of data. The orthology identification is restricted within each major clade only.

Any suggestions? Am I neglecting something?

Thank you very much,

Regards,

Tom

Answer 1

[Christophe Dessimoz]

You can use OMA (http://omabrowser.org) to retrieve orthologs between human and bacteria (or indeed across domains of life in general.

[wangdp123]

Thanks for this.

I have a quick look at the database but couldn't find the list of genomes that have been included in the database. Am I missing something?

[Christophe Dessimoz]

https://omabrowser.org/oma/release/

Answer 2

[h.mon]

You are correct, OrthoDB restricts orthologs by clade:

There are 290 orthology levels, that were retrieved from the NCBI Taxonomy (12): 116 eukaryotes (one for plants, 54 for animals, 60 for fungi), 136 for bacteria, 22 for archaea and 16 for viruses.

Quoted from the paper OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.