Figure 5. Thermodynamic modeling of cooperative interactions.

(A) Cooperative parameters were used to represent the energy gain (or loss) for pairs of factors that bind in proximity (up to 95 bp apart). (B) Binding probabilities for the five factors at the eve stripe 1 locus (chr2R:5873439-5874240), as inferred by the generalized hidden Markov model. (C) Ensemble of configurations sampled from the probabilities in (B). Each row (of the 100 shown) corresponds to one configuration, marking the positions of bound sites. (D) Cooperative parameters for nearby pairs of occupied binding sites, as optimized over the training set.