Game Theoretic Algorithms for Protein-DNA binding

We develop and analyze game-theoretic algorithms for predicting coordinate binding ofmultiple DNA binding regulators. The allocation of proteins to local neighborhoods andto sites is carried out with resource constraints while explicating competing and coordinate binding relations among proteins with affinity to the site or region. The focus of this paper is on mathematical foundations of the approach. Wealso briefly demonstrate the approach in the context of the λ-phage switch.