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MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs

Sacan, Ahmet
Ferhatosmanoglu, Nilgun
Ferhatosmanoglu, Hakan
Background: Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing. Description: An efficient and scalable search method for finding near-optimal dual-channel microarray designs, based on a greedy hill-climbing optimization strategy, has been developed. It is empirically shown that this method can successfully and efficiently find near-optimal designs. Additionally, an improved interwoven loop design construction algorithm has been developed to provide an easily computable general class of near-optimal designs. Finally, in order to make the best results readily available to biologists, a continuously evolving catalog of near-optimal designs is provided. Conclusion: A new search algorithm and database for near-optimal microarray designs have been developed. The search tool and the database are accessible via the World Wide Web at http:// db.cse.ohio-state.edu/MicroarrayDesigner. Source code and binary distributions are available for academic use upon request.