Game Theoretic Algorithms for Protein-DNA binding

Part of Advances in Neural Information Processing Systems 19 (NIPS 2006)

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Luis Pérez-breva, Luis E. Ortiz, Chen-hsiang Yeang, Tommi Jaakkola


We develop and analyze game-theoretic algorithms for predicting coordinate binding of multiple DNA binding regulators. The allocation of proteins to local neighborhoods and to 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. We also briefly demonstrate the approach in the context of the -phage switch.