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 <[EMAIL PROTECTED]> 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 > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Maximilian Haeussler, skype: maximilianhaeussler office: +33 1 69 82 41 29 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
