Karen S. Browning wrote:
>> Has anyone compliled an comparison of Arabidopsis initiation codon context
> for all these genes pouring out of the sequencing project? I would also be
> interested in comparisons of initiation codon context for other plants too.
> Is there a consensus sequence? Thanks for your help!
> Dr. Karen S. Browning
> Assistant Professor
> Department of Chemistry and Biochemistry
> University of Texas
> Austin, TX 78712
I am not aware of a real compilation but there is maybe
something better for you: a prediction program called
NetStart, which is working for Vertebrates or Arabidopsis
(separate options)and has been developed by A.G. Pedersen
in Denmark, using a clean dataset of Arabidopsis genes
as learning set.
It is available through the web at the following address:
try it !
To my own feeling (no validation), it detect quite many real
initiating ATG, especially for highly expressed genes, but
makes some false predictions too.
Pierre ROUZE Laboratoire Associe de l'INRA
Flanders Institute of Biotechnology - VIB - Department of Genetics
Universiteit Gent, K.L.Ledeganckstraat 35, B-9000 GENT, Belgium
mail:pirou at gengenp.rug.ac.be Tel: 32.9.264.5189
http://spider.rug.ac.be Fax: 32.9.264.5349