[BiO BB] Newbie question.

Maximilian Haeussler maximilianh at gmail.com
Tue Jan 8 05:50:52 EST 2008


Do you know to which transcription factor class this proteins belongs to?
They often bind to very similar / identical binding sites.
If you scan for with Interpro and do some research on pubmed about this
class (main classes: zinc finger, hemeobox, H2H, etc and their subclasses),
while keeping an eye on Transfac and Jaspar, you should come up with an idea
of the binding sites of your protein.
You can still do EMSAs afterwards...

But perhaps I've misunderstood the question...

cheers,
Max

On 06/01/2008, Donnie Darko <rabidstrikes at googlemail.com> wrote:
>
> Hi folks,
>
> Suppose I have a novel gene whose product is a DNA binding protein, how
> would I go about locating potential binding sites where this protein could
> bind? I'm only interested in finding sites for this specific protein and
> not
> a general scan of tfbs.
>
> I've extracted upstream sequences of genes that I'm interested in but I
> can't think of a way forward.
>
> Cheers and belated happy new year :-P
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> http://www.bioinformatics.org/mailman/listinfo/bbb
>



-- 
Maximilian Haeussler,
skype: maximilianhaeussler
office: +33 1 69 82 41 29



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