Question: Homologs between tomato and Arabidopsis
1
gravatar for I0110
9 months ago by
I011090
United States
I011090 wrote:

I was wondering if there is a database for the homologs between two plants. Specifically, I am looking for a list of homologs between tomato and Arabidopsis. Thanks!

homology genome • 429 views
ADD COMMENTlink modified 9 months ago by h.mon13k • written 9 months ago by I011090
2

Ensemble plants biomart is also a good source of orthologs. Also gives dn/ds.

ADD REPLYlink written 9 months ago by microfuge740

Thanks :-) It is just a little sad that the homologs are based on TAIR10 and an older version of Tomato transcriptome. I guess If I want to use the latest version of tomato annotation and Araport 11 annotation, I will have to blast them myself.

ADD REPLYlink written 9 months ago by I011090
1
gravatar for h.mon
9 months ago by
h.mon13k
Brazil
h.mon13k wrote:

Have you tried OrthoDB?

ADD COMMENTlink written 9 months ago by h.mon13k

It seems to me that the orthoDB is for checking few genes. Can we use it to generate a list of all homolog pairs between two species? Thanks!

ADD REPLYlink written 9 months ago by I011090
2

You can download bulk data and filter it yourself, or you can use SPARQL query - you can use the examples to build your query.

ADD REPLYlink written 9 months ago by h.mon13k
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