Question: Getting the highest taxonomy in the HOG database for a given OMA gene id
gravatar for yogihooda88
4 weeks ago by
yogihooda880 wrote:

I am trying to find how conserved a given gene is using the OMA database. I have a list of 500 genes and for each gene, I want to identify the last ancestor that has the HOG family a given gene belongs to? Does anybody know how do I go about doing that?

  • Yogesh
hog oma orthologs • 78 views
ADD COMMENTlink modified 4 weeks ago by Christophe Dessimoz540 • written 4 weeks ago by yogihooda880
gravatar for Christophe Dessimoz
4 weeks ago by
University College London
Christophe Dessimoz540 wrote:

There are several options. One way is to use the REST API. If you use e.g. P53_RAT as an input sequence:

You can see that the level is Chordata (in the current Dec 2018 release).

If you use Python, you can use the omadb package

$ pip install omadb

import omadb
from omadb import Client 
c = Client() 

Alternatively, still in Python, you could use the pyHam library for this (, and load the HOGs dynamically from the OMA browser (or from an OrthoXML file):

import pyham

my_gene_query = 'P53_RAT' 
pyham_analysis = pyham.Ham(query_database=my_gene_query, use_data_from='oma')

If you use the R, you can use our package OmaDB:


getHOG(id = 'P53_RAT', level='root')$level
ADD COMMENTlink written 4 weeks ago by Christophe Dessimoz540
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