[BiO BB] Newbie question.

[darx]

No, you are spot on.

So you mean that at best, we can narrow down to potential sites?

Cheers.

On 08/01/2008, Maximilian Haeussler <maximilianh at gmail.com> wrote:
>
> 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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> >
>
>
>
> --
> Maximilian Haeussler,
> skype: maximilianhaeussler
> office: +33 1 69 82 41 29
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