motif for TF within CTCF boundary

Hi,

I want to find motif for my TF within the CTCF boundary. I have some 200 genes where I want to do this analysis. I was wondering if there is any tool to identify my TF binding motif within CTCF boundaries for all the genes in one go without doing it manually.

Thanks,

Ankur

ctcf genome r

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updated 12.2 years ago by Alex Reynolds

• written 12.2 years ago by asharmatelome

1 answer

FIMO will search for TF binding sites within your sequences of interest.

As input, you will need: 1) sequences of interest, and 2) PWMs for your TFs of interest (e.g., JASPAR, TRANSFAC, UniPROBE, etc.).

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updated 6.6 years ago by Ram

• written 12.2 years ago by Alex Reynolds

Hi, How to determine the TAD boundary?

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written 6.0 years ago by BenHu •

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