Homologs between tomato and Arabidopsis

Question

[I0110]

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!

[microfuge]

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

[I0110]

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.

Answer 1

[h.mon]

Have you tried OrthoDB?

[I0110]

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!

[h.mon]

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