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Homologs between tomato and Arabidopsis

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
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updated by h.mon h.mon • written by I0110 I0110

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

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written by microfuge microfuge

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.

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written by I0110 I0110

1 answer

Have you tried OrthoDB?

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written by h.mon h.mon

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!

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written by I0110 I0110

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

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written by h.mon h.mon

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