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


METHODS
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.


CONCLUSIONS
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.
Sacan
Ahmet
A
Computer Engineering Department, Middle East Technical University, Ankara, Turkey. ahmet@ceng.metu.edu.tr
Ferhatosmanoglu
Nilgun
N
Ferhatosmanoglu
Hakan
H
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012107:Research Design; D012984:Software; D014584:User-Computer Interface