Engineering a scalable placement heuristic for DNA probe arrays
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Border Length Minimization in DNA Array Design
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Evaluation of Placement Techniques for DNA Probe Array Layout
Proceedings of the 2003 IEEE/ACM international conference on Computer-aided design
Approximating border length for DNA microarray synthesis
TAMC'08 Proceedings of the 5th international conference on Theory and applications of models of computation
Hardness and approximation of the asynchronous border minimization problem
TAMC'12 Proceedings of the 9th Annual international conference on Theory and Applications of Models of Computation
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The production of commercial DNA microarrays is based on a light-directed chemical synthesis driven by a set of masks or micromirror arrays. Because of the natural properties of light and the ever shrinking feature sizes, the arrangement of the probes on the chip and the order in which their nucleotides are synthesized play an important role on the quality of the final product. We propose a new model called conflict index for evaluating the layout of microarrays. We also present a new algorithm, called Pivot Partitioning, that improves the quality of layouts, according to existing measures, by over 6% when compared to the best known algorithms.