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Nucleic Acids Research 2005 33(17):e144; doi:10.1093/nar/gni147
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Published online 28 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Methods Online

A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays

Kang Ning, Kwok Pui Choi1, Hon Wai Leong and Louxin Zhang2,*

Department of Computer Science, National University of Singapore Singapore 117543 1Department of Statistics and Applied Probability, National University of Singapore Singapore 117543 2Department of Mathematics, National University of Singapore Singapore 117543

*To whom correspondence should be addressed. Tel: +65 6874 6579; Fax: +65 6779 5452; Email: matzlx{at}nus.edu.sg

Received May 26, 2005. Revised July 31, 2005. Accepted September 15, 2005.

The broad applicability of gene expression profiling to genomic analyses has generated huge demand for mass production of microarrays and hence for improving the cost effectiveness of microarray fabrication. We developed a post-processing method for deriving a good synthesis strategy. In this paper, we assessed all the known efficient methods and our post-processing method for reducing the number of synthesis cycles for manufacturing a DNA-chip of a given set of oligos. Our experimental results on both simulated and 52 real datasets show that no single method consistently gives the best synthesis strategy, and post-processing an existing strategy is necessary as it often reduces the number of synthesis cycles further.


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