transcription factor binding site prediction tool - (Mar/30/2012 )
I am working with novel protein which has dna binding motifs (Zn finger) and trying to relate this protein to transcription. There is no publication investigating its transcription target genes so I don't know how I can start to test its transcription activity. I just wonder if there is any tool for the prediction of Zn finger binding sites available? Also wonder if any reporter (luciferase) construct available to see if Zn finger motifs of my protein can activate gene transcription by binding to the Zn finger binding sites on the plasmid. Thanks in advance!
that's my first google hit ...i'm no expert on this field but i'm sure there are plenty of papers or even predictions since Zn finger binding motifs are one of the best understood dna binding motifs and even used for site specific integration in eukaryotes ...so people can design them and therefore they need to understand and predict.
You will for sure find a proper prediction program ...but you'll have to spend some time on this!