Question

Homologs between tomato and Arabidopsis

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6.8 years ago

I0110 ▴ 140

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!

genome homology • 2.5k views

ADD COMMENT • link updated 6.8 years ago by h.mon 35k • written 6.8 years ago by I0110 ▴ 140

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

ADD REPLY • link 6.8 years ago by microfuge ★ 1.9k

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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 REPLY • link 6.8 years ago by I0110 ▴ 140

score 1 · Answer 1 · 2017-07-17

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6.8 years ago

h.mon 35k

Have you tried OrthoDB?

ADD COMMENT • link 6.8 years ago by h.mon 35k

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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 REPLY • link 6.8 years ago by I0110 ▴ 140

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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 REPLY • link 6.8 years ago by h.mon 35k