<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>

CC BY-SA 4.0
2019-06-04T02:31:35.953Z
2019-06-04T02:31:35.953Z
Alex Reynolds
<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>

CC BY-SA 4.0
2019-06-04T02:38:39.117Z
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)
Alex Reynolds
<bioconductor><genome><proteins><computation><transposable-elements>
How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene?
# 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)  

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## 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.


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