motif for TF within CTCF boundary

Question

[asharmatelome]

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

Answer 1

[Alex Reynolds]

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.).

[BenHu]

Hi, How to determine the TAD boundary?