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

Nucleic Acids Res. 2005 Sep 28;33(17):e144. doi: 10.1093/nar/gni147.


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.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Composition
  • Computational Biology / methods
  • Gene Expression Profiling*
  • Oligonucleotide Array Sequence Analysis*
  • Oligonucleotide Probes / chemical synthesis*
  • Oligonucleotide Probes / chemistry


  • Oligonucleotide Probes