Identifying Transcription Factor Binding Sites From Chip Seq

Question

[ancient_learner]

hiii i have a set of filtered Mirna which we believe are important. i want to examine whether these Mirna have any TF binding sites (particularly for a protein) in <2kb region. how do i do it with the help of chip seq? Thank you in advance

[Ido Tamir]

Please explain more about the chip-seq data (?) you have.

Answer 1

[Davy]

Filter your sequence data to contain the upstream seqeunces of the mirnas you are interested in, and then use a program like MEME http://meme.sdsc.edu/meme/intro.html for either checking for known sites, or for motif discovery.