[Feedback] Site Feedback: comparative data across different species

[Marcela K. Monaco]

Dear Sanzhen,

You may obtain a list of orthologues (or paralogues) for any gene from its
Gene Summary page, for example see
http://ensembl.gramene.org/Zea_mays/Gene/Summary?db=core;g=GRMZM2G469469;r=2:234351781-234357920;t=GRMZM2G469469_T01

Note: To get to the Gene Summary page, I simply entered the gene name
("bt1") in the Gramene search box and clicked on the result and selected
"zea mays" as species as shown in
http://tools.gramene.org/search?query=bt1&fq=species~zea_mays

If you click on the "Ortologues" (n=47) link or the "Paralogues" (n=8) on
the left navigation bar of the Gene page, a table including orthologues for
the bt1 gene will appear on your browser and this can be easily downloaded
by clicking on the "Excel" icon onthe top right corner of the table.

Alternatively, you may get a list of orthologues for a list of genes in
certain species by using the customizable Gramene Mart platform, see
http://ensembl.gramene.org/biomart/martview as follows:

1. Select "Plant Genes (42)" and the dataset of interest, [Zea mays genes
(AGPv3 (5b))] in this case.
2. Under "Filters", select "Gene"
3. Copy or upload a gene or a list of gene IDS in the "ID list limit" filter
4. Under "Attributes", select "Homologs" and then the species for which you
want homologs under "Orthologs" or "Paralogs" (Other options such as %
identity are available under "Gene"

Please let us know if we can be of further assistance.  Thanks!

Marcela




On Tue, Oct 7, 2014 at 5:58 PM, feedback at gramene.org <feedback at gramene.org>
wrote:

> URL         : http://www.gramene.org/ftp-download
>
> Subject     : Site Feedback: comparative data across different species
>
> Name        : Sanzhen Liu
>
> Email       : liu3zhen at ksu.edu
>
> Organization: Kansas State University
>
> Comments    :
>
> Dear sir/madam,
>
> I spent much time to look for a table containing ortholog information
> across species. Could you guide me to find that data in your database.
> Appreciate your help.
>
> Thanks,
>
> -Sanzhen
>
> http://www.warelab.org/bugs/view.php?id=5044
>
>
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>
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