Question: Homologs between tomato and Arabidopsis
1
gravatar for I0110
2.4 years ago by
I0110120
United States
I0110120 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 • 960 views
ADD COMMENTlink modified 2.4 years ago by h.mon29k • written 2.4 years ago by I0110120
2

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

ADD REPLYlink written 2.4 years ago by microfuge1.5k

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 2.4 years ago by I0110120
1
gravatar for h.mon
2.4 years ago by
h.mon29k
Brazil
h.mon29k wrote:

Have you tried OrthoDB?

ADD COMMENTlink written 2.4 years ago by h.mon29k

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 2.4 years ago by I0110120
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 2.4 years ago by h.mon29k
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