Question: Homologs between tomato and Arabidopsis
1
gravatar for hwu12
11 days ago by
hwu1250
United States
hwu1250 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 • 126 views
ADD COMMENTlink modified 11 days ago by h.mon7.5k • written 11 days ago by hwu1250
2

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

ADD REPLYlink written 10 days ago by microfuge610

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 10 days ago by hwu1250
1
gravatar for h.mon
11 days ago by
h.mon7.5k
Brazil
h.mon7.5k wrote:

Have you tried OrthoDB?

ADD COMMENTlink written 11 days ago by h.mon7.5k

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 11 days ago by hwu1250
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 11 days ago by h.mon7.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1166 users visited in the last hour