text: user3968: 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?
  
  user776: 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.
  
original_text: 3968: <p>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?</p>
  
  <p>Are there any Bioinformatic tools available for this task?</p>
   776: <p>You could run <a href="http://meme-suite.org/doc/fimo.html" rel="nofollow noreferrer">FIMO</a> on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you binding sites: genomic intervals where those TFs bind.</p>
  
  <p><a href="https://bioinformatics.stackexchange.com/a/2491/776">https://bioinformatics.stackexchange.com/a/2491/776</a></p>
  
  <p>You can then map or intersect promoter regions with those TF binding sites with BEDOPS <code>bedmap</code> or <code>bedops</code>, respectively:</p>
  
  <p><a href="https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html" rel="nofollow noreferrer">https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html</a></p>
  
  <p><a href="https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html" rel="nofollow noreferrer">https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html</a></p>
  
  <p>The use of <code>bedmap</code> 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.</p>
  