What is the best tool to use to get the genomic coordinates (as a BED file) of the binding sites of a transcription factor? I would like to do this genomewide.
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sumithrasank75
I don't know if it is the "best", but a popular tool is FIMO, from the MEME suite.
For command-line work, you provide the FASTA of your genome of interest and your TF model(s) in MEME format, e.g. from JASPAR, UniPROT, TRANSFAC, etc.
A 10^-4 or -5 threshold is probably reasonable for whole-genome work; a more stringent threshold will give you fewer binding sites.
I agree. This is an area that I have been working on recently, particularly both JASPAR and TRANSFAC.
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