Identify TF binding sites genomewide

Question

[sumithrasank75]

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.

Answer 1

[Alex Reynolds]

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.

[Kevin Blighe]

I agree. This is an area that I have been working on recently, particularly both JASPAR and TRANSFAC.