title: Optimum DNA curvature using a hybrid approach involving an artificial neural network and genetic algorithm.
abstract: In the present paper, a hybrid technique involving artificial neural network (ANN) and genetic algorithm (GA) has been proposed for performing modeling and optimization of complex biological systems. In this approach, first an ANN approximates (models) the nonlinear relationship(s) existing between its input and output example data sets. Next, the GA, which is a stochastic optimization technique, searches the input space of the ANN with a view to optimize the ANN output. The efficacy of this formalism has been tested by conducting a case study involving optimization of DNA curvature characterized in terms of the RL value. Using the ANN-GA methodology, a number of sequences possessing high RL values have been obtained and analyzed to verify the existence of features known to be responsible for the occurrence of curvature. A couple of sequences have also been tested experimentally. The experimental results validate qualitatively and also near-quantitatively, the solutions obtained using the hybrid formalism. The ANN-GA technique is a useful tool to obtain, ahead of experimentation, sequences that yield high RL values. The methodology is a general one and can be suitably employed for optimizing any other biological feature.
authors.affiliation: Chemical Engineering Division, National Chemical Laboratory, Pune, India.
authors.forename: R V
authors.initials: RV
authors.lastname: Parbhane
authors.forename: S
authors.initials: S
authors.lastname: Unniraman
authors.forename: S S
authors.initials: SS
authors.lastname: Tambe
authors.forename: V
authors.initials: V
authors.lastname: Nagaraja
authors.forename: B D
authors.initials: BD
authors.lastname: Kulkarni
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008957:Models, Genetic; D009154:Mutation; D016571:Neural Networks, Computer; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA