AUG context

[Pierre Rouze]

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:

        http://www.cbs.dtu.dk/services/NetStart/

        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

--
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