Question: Identify TF binding sites genomewide
0
gravatar for sumithrasank75
13 months ago by
United States
sumithrasank75130 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 • 415 views
ADD COMMENTlink modified 13 months ago by Alex Reynolds28k • written 13 months ago by sumithrasank75130
3
gravatar for Alex Reynolds
13 months ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k 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 COMMENTlink modified 13 months ago • written 13 months ago by Alex Reynolds28k

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

ADD REPLYlink written 13 months ago by Kevin Blighe41k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1483 users visited in the last hour