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!
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written
by
liuxiaomeng90 •
1 answer
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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written
by
Felix Francis
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