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.
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?
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.
The suggested fimo approach is a bash one-liner on the command line. You won't find anything simpler :)
Cross-posting the same question is generally discouraged. You could easily edit your Bioinformatics SE question to include these new parameters.
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.
You can then map or intersect promoter regions with those TF binding sites with BEDOPS bedmap or bedops, respectively:
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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