[Feedback] Site Feedback: extracting more than one snp

[Marcela K. Monaco]

Hi Christine,

Thanks for the compliments.

There are a couple of ways to extract SNP data from Gramene.  One is via
the genome browser (http://ensembl.gramene.org/genome_browser/), which is
only practical if you are interested in one gene.  The other one is the
Gramene Mart utility at http://ensembl.gramene.org/biomart/martview which
allows you query a single gene, a set of genes (just make a list) or genes
within a genomic region.

On the browser, you need to go to your gene of interest (e.g.,
http://ensembl.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=OS05G0113900;r=5:726144-751143;t=OS05T0113900-01),
then from the left side bar select "Variation table" (or image) and "Export
Data".  Even more informative it might be the gene's corresponding
"Transcript" page (e.g.,
http://ensembl.gramene.org/Oryza_sativa/Transcript/Summary?db=core;g=OS05G0113900;r=5:726144-751143;t=OS05T0113900-01),
click on "Variations" and then on the little Excel table icon on the top
right corner of the Variations table.  Or "Export Data"

On the Mart, select the "Plant Variation" database, then species, and
appropriate filters (including specifying a list of genes if you so
desired).

Have fun!  Let me know if you need any further assistance.

Marcela


==
Marcela Karey Monaco, PhD
Gramene Project Coordinator
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-8808
Fax: 516-367-6851


On Thu, Aug 21, 2014 at 12:47 PM, feedback at gramene.org <feedback at gramene.org
> wrote:

> URL         : http://ensembl.gramene.org/tools.html
>
> Subject     : Site Feedback: extracting more than one snp
>
> Name        : Christine Hainey
>
> Email       : christine.f.hainey at usa.dupont.com
>
> Organization: DuPont-Pioneer
>
> Comments    :
>
> Hi,
> Gramene is very useful.  I like the interface.
>
> One feature I have not found, or is not provided, is the ability to
> extract snps from a gene.  I can curretnly extract snps one at a time, but
> I would like to be able to do a whole gene, or large interval.
>
> thanks,
> christine
>
> http://www.warelab.org/bugs/view.php?id=5013
>
>
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> Feedback mailing list
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> http://brie4.cshl.edu/mailman/listinfo/feedback
>
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