Are there any programs out there that can identify which specific DNA motif a transcription factor binds to, given the entire promoter sequence and TF sequence/structure.
I've got the promoter sequence which I know the transcription factor binds to, and I have the protein sequence and putative structure of the transcription factor, so have a good idea what the DNA-binding domain looks like. I'd like to be able to show specifically where in the promoter the it binds, does the software exist to be able to predict this?
As a side note, does binding site of the transcription factor have any kind of relationship to the -35 and -10 boxes? For example does it have a preference for binding upstream of these regions, or is it just as likely to bind anywhere on the promoter?
There are many predictors around on the web.
You could try Transfac from Biobase.
Results from these tools are very disappointing, you will find binding sites everywhere.
But you might get an idea and do mutagenisis to find out what is the real binding site of your protein, by doing shift assays and/or reporter assays.
Below, I add several links.
http://omictools.com/protein-dna-interaction-prediction-category
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763535/
http://www.ncbi.nlm.nih.gov/pubmed/21689482
As Martin correctly said, the programs only give you a first indication of what might be the binding sequence.
You always need the experiment to find out. Also, some transcription factors bind far away from the promoter boxes! Do gel band shift assays etc. A very exact, but old method is DNase I footprinting.
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