Question: Use OrthoDB to retrieve the orthologs between human and bacteria
0
gravatar for wangdp123
4 weeks ago by
wangdp123120
Oxford
wangdp123120 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 • 96 views
ADD COMMENTlink modified 5 days ago by Christophe Dessimoz480 • written 4 weeks ago by wangdp123120
1
gravatar for Christophe Dessimoz
5 days ago by
University College London
Christophe Dessimoz480 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 5 days ago by Christophe Dessimoz480

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 5 days ago by wangdp123120
0
gravatar for h.mon
4 weeks ago by
h.mon20k
Brazil
h.mon20k 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 4 weeks ago by h.mon20k
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