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Question: How to find the binding sites for a particular transcription factor among the human genome
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gravatar for liuxiaomeng90
5.5 years ago by
liuxiaomeng90 • 70
China
liuxiaomeng90 • 70 wrote:

I want to find the binding sites for a particular transcription factor among the whole genome. Maybe the results could be something like bed files which indicate the potential TFBS. I read some question about finding TFBS. But most of the question is about finding potential transcription factor in a certain gene region. If there's any software can do such thing?

Thanks!
tfbs • 2.2k views
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modified 5.5 years ago by Felix Francis • 510 • written 5.5 years ago by liuxiaomeng90 • 70
1
gravatar for Felix Francis
5.5 years ago by
Felix Francis • 510
United States/University of Delaware
Felix Francis • 510 wrote:

You could use TRANSFAC database to construct specific binding site weight matrices, which can then be used for your TFBS prediction.

There are several tools that do this. example: PROMO, TRANSFAC, JASPER. For tools that predict all the possible TFBS, you could just parse the result to get only the sites for a particular transcription factor of interest.
ADD COMMENT • link written 5.5 years ago by Felix Francis • 510
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