Size of binding site

[chip_seq]

Hi all,

How can i know the size of binding site of a protein that is known to bind DNA considering that i've ChIP_Seq data for that protein.

Thanks in advance.

[giror]

You could find a consensus motif from all of the bound sites using MEME. Then you will see the irrelevant bases on the sides because they will have low informaiton content. Most TF binding sites are 6-8 bases so if you set the window length to 10 or 11 you should be good. any longer and it is a real combinatorial explosion.