Question: Use OrthoDB to retrieve the orthologs between human and bacteria
0
gravatar for wangdp123
11 weeks ago by
wangdp123140
Oxford
wangdp123140 wrote:

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

orthodb orthologs • 154 views
ADD COMMENTlink modified 8 weeks ago by Christophe Dessimoz500 • written 11 weeks ago by wangdp123140
1
gravatar for Christophe Dessimoz
8 weeks ago by
University College London
Christophe Dessimoz500 wrote:

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

ADD COMMENTlink written 8 weeks ago by Christophe Dessimoz500

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?

ADD REPLYlink written 8 weeks ago by wangdp123140
0
gravatar for h.mon
11 weeks ago by
h.mon21k
Brazil
h.mon21k wrote:

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.

ADD COMMENTlink written 11 weeks ago by h.mon21k
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