Question: Can HOMER be used to predict the binding site of a transcription factor on a DNA sequence?
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gravatar for charlesgwellem
16 months ago by
charlesgwellem0 wrote:

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.

homer rna-seq chip-seq gene genome • 636 views
ADD COMMENTlink modified 16 months ago by Alex Reynolds30k • written 16 months ago by charlesgwellem0

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?

ADD REPLYlink written 16 months ago by ATpoint38k

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.

ADD REPLYlink written 16 months ago by charlesgwellem0
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The suggested fimo approach is a bash one-liner on the command line. You won't find anything simpler :)

ADD REPLYlink written 16 months ago by ATpoint38k

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

ADD REPLYlink written 16 months ago by Alex Reynolds30k
1
gravatar for Alex Reynolds
16 months ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

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.

ADD COMMENTlink written 16 months ago by Alex Reynolds30k
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