Can HOMER be used to predict the binding site of a transcription factor on a DNA sequence?

Question

[charlesgwellem]

I wish to find out if HOMER tool can be used to predict the binding site of a transcription factor on a list of DNA sequences.

Thank you in advance for your kind and helpful responses.

[ATpoint]

Cross-posted at SE: https://bioinformatics.stackexchange.com/questions/8691/how-do-i-computationally-predict-the-binding-position-of-a-dna-binding-protein-o/

You already received answers there, what about them?

[charlesgwellem]

Ok thanks saw it. I wish to find out about the existence of a simple user-friendly online tool, or an R package rather than methods that are more computationally intensive.

[ATpoint]

The suggested fimo approach is a bash one-liner on the command line. You won't find anything simpler :)

[Alex Reynolds]

Cross-posting the same question is generally discouraged. You could easily edit your Bioinformatics SE question to include these new parameters.

Answer 1

[Alex Reynolds]

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.