How do I computationally predict the binding position of a DNA binding protein on the promoters of differentially expressed genes? I have a list of human genes that have been proven to be up-regulated in a disease condition of interest, using microarray analysis. I also have a protein which according to literature is said to be a DNA binding protein. I wish to be able to computationally predict if the protein mentioned binds to any of the promoter sequences of my differentially expressed genes and if yes , then at which position?

Are there any Bioinformatic tools available for this task?
You could run FIMO on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you binding sites: genomic intervals where those TFs bind.

https://bioinformatics.stackexchange.com/a/2491/776

You can then map or intersect promoter regions with those TF binding sites with BEDOPS bedmap or bedops, respectively:

https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html

The use of bedmap is recommended to assign TFs to a promoter of interest. This tool will return both the promoter region and any TFs that overlap it by the specified overlap criteria.