est database search

[Dave Matthews]

Hi Manoj,

Two answers.  

First
To find ESTs for glutenins and gliadins, I think the most useful way for your
purpose would be to BLAST a glutenin or gliadin sequence such as AY367771 at
http://www.graingenes.org/cgi-bin/ace/custom/goBlast/graingenes, against the
database "Consensus sequences from Wheat SNP Assembly, dec02".

The result will be a list of EST contigs, already aligned and ready for SNP
searching.


Second
To find ESTs from developing wheat seeds.  Go to 
http://wheat.pw.usda.gov/cgi-bin/westsql/sql.cgi and enter the following
query in the SQL box:
select name, genus, tissue, stage from est_lib where genus like "Triticum"

In the resulting table find the libraries you're interested in, e.g.
CSB1, from "endosperm, mid-development".  Now go to 
http://wheat.pw.usda.gov/cgi-bin/westsql/est_lib.cgi and search for
each of these libraries.  (You can only search for one at a time.)


Also, you might find it helpful to look at the Wheat SNP Development page,
http://wheat.pw.usda.gov/ITMI/WheatSNP/.  Some of the contigs from the
"Consensus sequences from Wheat SNP Assembly, dec02" BLAST database are 
already being searched for SNPs by other groups.  Click on the link
"Allocation of the sugar plums" to see which ones these are.

best regards,
- Dave


> From: "manoj oak" <manojoak at hotmail.com>
> To: gramene at gramene.org
> Subject: est database search
> Date: Sat, 11 Oct 2003 11:31:05 +0530
> 
> Dear graingenes,
> i am interested in glutenin and gliadin ESTs of wheat. I want to do SNPs 
> detection and construction of allele specific primers for these proteins. 
> this is useful in breeding, enduse quality detection, and varietal 
> identification.
> is any body know where i can get all the wheat ests which are obtained from 
> developing seeds.
> looking forward to your positive reply
> yours
> Manoj Dinesh Oak
> Plant Molecular Biology
> Genetics Department
> Plant Molecular Biology Group
> Agharkar Research Institute
> Agarkar Road
> Pune 411 004
> India