How to find the binding sites for a particular transcription factor among the human genome
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6.2 years ago

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 • 2.4k views
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6.2 years ago
Felix Francis ▴ 550

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.

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