  A mesoscopic model which allows us to identify and quantify the strength of
binding sites in DNA sequences is proposed. The model is based on the
Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle
which explores the sequence interacting more importantly with open base pairs
of the DNA chain. We apply the model to promoter sequences of different
organisms. The free energy landscape obtained for these promoters shows a
complex structure that is strongly connected to their biological behavior. The
analysis method used is able to quantify free energy differences of sites
within genome sequences.
