<div dir="ltr"><div><div>Hi Christine,<br><br></div>Thanks for the compliments. <br><br>There are a couple of ways to extract SNP data from Gramene. One is via the genome browser (<a href="http://ensembl.gramene.org/genome_browser/">http://ensembl.gramene.org/genome_browser/</a>), which is only practical if you are interested in one gene. The other one is the Gramene Mart utility at <a href="http://ensembl.gramene.org/biomart/martview">http://ensembl.gramene.org/biomart/martview</a> which allows you query a single gene, a set of genes (just make a list) or genes within a genomic region.<br>
<br></div>On the browser, you need to go to your gene of interest (e.g., <a href="http://ensembl.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=OS05G0113900;r=5:726144-751143;t=OS05T0113900-01">http://ensembl.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=OS05G0113900;r=5:726144-751143;t=OS05T0113900-01</a>), 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., <a href="http://ensembl.gramene.org/Oryza_sativa/Transcript/Summary?db=core;g=OS05G0113900;r=5:726144-751143;t=OS05T0113900-01">http://ensembl.gramene.org/Oryza_sativa/Transcript/Summary?db=core;g=OS05G0113900;r=5:726144-751143;t=OS05T0113900-01</a>), click on "Variations" and then on the little Excel table icon on the top right corner of the Variations table. Or "Export Data"<br>
<div><br></div><div>On the Mart, select the "Plant Variation" database, then species, and appropriate filters (including specifying a list of genes if you so desired).<br><br></div><div>Have fun! Let me know if you need any further assistance.<br>
<br></div><div>Marcela<br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><font size="1">==<br>
Marcela Karey Monaco, PhD</font> <font size="1"><br>Gramene Project Coordinator<br>Cold Spring Harbor Laboratory<br>One Bungtown Road, Williams #5<br>Cold Spring Harbor, NY 11724<br></font></span><span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><font size="1">Phone: <a value="+15163676998" style="color:rgb(17,85,204)"><span>516</span>-<span>367</span>-<span><span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial"><span><font size="1">8808</font></span></span></span></a><a value="+15163676998" style="color:rgb(17,85,204)"><span></span></a><br>
Fax: <a value="+15163676851" style="color:rgb(17,85,204)"><span>516</span>-<span>367</span>-6851</a></font></span></div>
<br><br><div class="gmail_quote">On Thu, Aug 21, 2014 at 12:47 PM, <a href="mailto:feedback@gramene.org">feedback@gramene.org</a> <span dir="ltr"><<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">URL : <a href="http://ensembl.gramene.org/tools.html" target="_blank">http://ensembl.gramene.org/tools.html</a><br>
<br>
Subject : Site Feedback: extracting more than one snp<br>
<br>
Name : Christine Hainey<br>
<br>
Email : <a href="mailto:christine.f.hainey@usa.dupont.com">christine.f.hainey@usa.dupont.com</a><br>
<br>
Organization: DuPont-Pioneer<br>
<br>
Comments :<br>
<br>
Hi,<br>
Gramene is very useful. I like the interface.<br>
<br>
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.<br>
<br>
thanks,<br>
christine<br>
<br>
<a href="http://www.warelab.org/bugs/view.php?id=5013" target="_blank">http://www.warelab.org/bugs/view.php?id=5013</a><br>
<br>
<br>
_______________________________________________<br>
Feedback mailing list<br>
<span class="HOEnZb"><font color="#888888"><a href="mailto:Feedback@gramene.org">Feedback@gramene.org</a><br>
<a href="http://brie4.cshl.edu/mailman/listinfo/feedback" target="_blank">http://brie4.cshl.edu/mailman/listinfo/feedback</a><br>
</font></span></blockquote></div><br></div>