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Question: Identify TF binding sites genomewide
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gravatar for sumithrasank75
2.1 years ago by
sumithrasank75 • 130
United States
sumithrasank75 • 130 wrote:

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.
next-gen sequence genome • 656 views
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modified 2.1 years ago by Alex Reynolds ♦ 29k • written 2.1 years ago by sumithrasank75 • 130
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gravatar for Alex Reynolds
2.1 years ago by
Alex Reynolds ♦ 29k
Seattle, WA USA
Alex Reynolds ♦ 29k wrote:

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.
ADD COMMENT • link modified 2.1 years ago • written 2.1 years ago by Alex Reynolds ♦ 29k

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

ADD REPLY • link written 2.1 years ago by Kevin Blighe ♦ 56k
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