Answers.Body: <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 predicted binding sites: genomic intervals where those TFs bind, with some statistical significance.</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>You can define your promoter regions however you like, e.g., from the TSS to 2.5kb upstream of the TSS. It's up to you and your experiment.</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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-04T02:31:35.953Z
Answers.LastActivityDate: 2019-06-04T02:31:35.953Z
Answers.UserDisplayName: Alex Reynolds
Body: <p>Is there any computational tool or any other method to predict if the binding site of DNA binding protein is actually located on a promoter sequence?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-04T02:38:39.117Z
Comments.Text: Possible duplicate of [How do I computationally predict the binding position of a DNA binding protein on the promoters of differentially expressed genes?](https://bioinformatics.stackexchange.com/questions/8691/how-do-i-computationally-predict-the-binding-position-of-a-dna-binding-protein-o)
Comments.UserDisplayName: Alex Reynolds
Tags: <bioconductor><genome><proteins><computation><transposable-elements>
Title: How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?
ThreadText: # How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?
  
  (Asked by: username_0 on 2019-06-03)
  
  Is there any computational tool or any other method to predict if the binding site of DNA binding protein is actually located on a promoter sequence?
  
  **Tags:** bioconductor, genome, proteins, computation, transposable-elements
  
  > **Comments:**
  > **username_1**: Possible duplicate of [How do I computationally predict the binding position of a DNA binding protein on the promoters of differentially expressed genes?](https://bioinformatics.stackexchange.com/questions/8691/how-do-i-computationally-predict-the-binding-position-of-a-dna-binding-protein-o)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-06-04. Score: 1
  
  You could run [FIMO](http://meme-suite.org/doc/fimo.html) on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you predicted binding sites: genomic intervals where those TFs bind, with some statistical significance.
  
  <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>
  
  You can define your promoter regions however you like, e.g., from the TSS to 2.5kb upstream of the TSS. It's up to you and your experiment.
  
  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.
  
  
  ---
  
  