[Gramene] wheat rice comparison

[Somers, Daryl]

OK, thanks for the suggestions to various Gramene people, I'll work
through it, and let you know if I hit a wall.

D

Daryl J. Somers
Agriculture and Agri-Food Canada
Cereal Research Centre
195 Dafoe Road
Winnipeg, MB, Canada
R3T 2M9
phone: 204-984-4503
fax: 204-983-4604
 
SomersD at agr.gc.ca
 
 Agriculture and Agri-Food Canada - Agriculture et Agroalimentaire
Canada

-----Original Message-----
From: Chengzhi Liang [mailto:liang at cshl.edu] 
Sent: March 14, 2008 2:01 PM
To: Somers, Daryl
Cc: gramene-dev at gramene.org; gramene at gramene.org
Subject: Re: [Gramene] wheat rice comparison


Hi Daryl,

There are a couple ways to do this. One is to search our markers 
database (or whole Gramene) using the generic search function on each 
page. If you can find the the sequence in the markers module, you will 
then be able to get the alignments through the links on the marker 
information page (you will see this if your search return results). The 
second way is to use BLAST on the blast search page. Copy and paste your

sequence there, choose TBLATX and rice genome. There will be genome 
locations on the result page. Through the links on chromosome there and 
go to genome browser detail page, turn on wheat EST track to see if your

sequence is there. If none of these work, try to use exonerate 
(http://www.ebi.ac.uk/~guy/exonerate/) program do your own alignments.

Chengzhi

Somers, Daryl wrote:

> Hello Gramene
>
>  
>
> Please provide me with the process and route through the Gramene site 
> to do the following.
>
>  
>
> Start with a Wheat EST accession number
>
> Compare this (sequence) to the Rice genome sequence and
>
> Finish with a wheat/rice sequence alignment showing the proposed wheat

> intron/exon boundaries.
>
>  
>
> I want to develop PCR primers from the wheat coding sequence that 
> likely span an intron.
>
>  
>
> Please indicate which features etc need to be on/off.
>
>  
>
> Hope you can help.
>
>  
>
> Regard
>
>  
>
>  
>
>  
>
> Daryl J. Somers
>
> Agriculture and Agri-Food Canada
>
> Cereal Research Centre
>
> 195 Dafoe Road
>
> Winnipeg, MB, Canada
>
> R3T 2M9
>
> phone: 204-984-4503
>
> fax: 204-983-4604
>
>  
>
> SomersD at agr.gc.ca <mailto:SomersD at agr.gc.ca>
>
>  
>
> Agriculture and Agri-Food Canada - Agriculture et Agroalimentaire
Canada
>
>  
>
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