rice and arabidopsis promoters

[Gregory S. Brown]

Stuart,

The MartView system in gramene can help with data extraction problems  
like this.  Start here:  http://www.gramene.org/Multi/martview  and  
select the species dataset you need.  Then the next page allows you  
to restrict the dataset of extracted genes by many different  
criteria.  Since you are interested in all gene sequences simply  
proceed on to the next page by hitting the "next" button again.   
Notice on the right hand side the resulting number of gene models  
from the selected dataset you are working with.  For Arabidopsis  
TAIR6 gene models there are 30,569 entries in the db.  Now to extract  
sequence data for the selected gene models you must select  
"Sequences" from the "Select Attribute Page menu at the very top of  
this page.  Notice all the different types of  sequences you can  
choose that include where appropriate upstream and downstream  
flanking regions.  Input in the size of the flanking regions and then  
select appropriate fasta header information to include in the  
extracted sequence.  Hit the export button to extract the information  
you need.

There is a good help page for the MartView system.  In fact there is  
an excellent help section for most pages in gramene.  Simply find the  
red "Help Desk" button located generally on the upper right hand side  
of most pages.  Then look at the list of help topics on the left hand  
side.

Hope this helps.

gb
Greg Brown

On Sep 18, 2006, at 8:22 AM, Stuart Meier wrote:

> To whom it may concern,
> I am a post-doctoral fellow at The University of the Western Cape in
> South Africa.  I am trying to download promoter sequences for
> arabidopsis and rice (oryza sativa) from the gramene website without
> success.  I require nucleotide sequences    -3000 to +500, relative to
> the transcription start sie, for all genes in the genome.  Could  
> you be
> kind enough to inform me if this is possible your web site and provide
> some directions on how this could be done.
> your help will be greatly appreciated
> regards
> Dr Stuart Meier
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