Bioinformatics Vol. 17 no. 11 2001
Pages 1067-1076
© 2001 Oxford University Press
Selection of optimal DNA oligos for gene expression arrays
Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
Received on January 11, 2001
; revised on May 29, 2001
; accepted on May 29, 2001
Motivation: High density DNA oligo microarrays are widely used in biomedical research. Selection of optimal DNA oligos that are deposited on the microarrays is critical. Based on sequence information and hybridization free energy, we developed a new algorithm to select optimal short (20–25 bases) or long (50 or 70 bases) oligos from genes or open reading frames (ORFs) and predict their hybridization behavior. Having optimized probes for each gene is valuable for two reasons. By minimizing background hybridization they provide more accurate determinations of true expression levels. Having optimum probes minimizes the number of probes needed per gene, thereby decreasing the cost of each microarray, raising the number of genes on each chip and increasing its usage.
Results: In this paper we describe algorithms to optimize the selection of specific probes for each gene in an entire genome. The criteria for truly optimum probes are easily stated but they are not computable at all levels currently. We have developed an heuristic approach that is efficiently computable at all levels and should provide a good approximation to the true optimum set. We have run the program on the complete genomes for several model organisms and deposited the results in a database that is available on-line (http://ural.wustl.edu/~lif/probe.pl).
Availability: The program is available upon request.
Contact: lif{at}ural.wustl.edu; stormo{at}ural.wustl.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. J. Harriff, M. Wu, M. L. Kent, and L. E. Bermudez Species of Environmental Mycobacteria Differ in Their Abilities To Grow in Human, Mouse, and Carp Macrophages and with Regard to the Presence of Mycobacterial Virulence Genes, as Observed by DNA Microarray Hybridization Appl. Envir. Microbiol., January 1, 2008; 74(1): 275 - 285. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Wu, H. Zhao, K. Baggerly, R. Carta, and L. Zhang Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays Bioinformatics, October 1, 2007; 23(19): 2566 - 2572. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Paredes, R. S. Senger, I. S. Spath, J. R. Borden, R. Sillers, and E. T. Papoutsakis A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum Appl. Envir. Microbiol., July 15, 2007; 73(14): 4631 - 4638. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Mehlmann, E. D. Dawson, M. B. Townsend, J. A. Smagala, C. L. Moore, C. B. Smith, N. J. Cox, R. D. Kuchta, and K. L. Rowlen Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus. J. Clin. Microbiol., August 1, 2006; 44(8): 2857 - 2862. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Yamada, H. Soma, and S. Morishita PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W665 - W669. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Liebich, C. W. Schadt, S. C. Chong, Z. He, S.-K. Rhee, and J. Zhou Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental Applications Appl. Envir. Microbiol., February 1, 2006; 72(2): 1688 - 1691. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. C. Tilton, L. G. Gerwick, J. D. Hendricks, C. S. Rosato, G. Corley-Smith, S. A. Givan, G. S. Bailey, C. J. Bayne, and D. E. Williams Use of a Rainbow Trout Oligonucleotide Microarray to Determine Transcriptional Patterns in Aflatoxin B1-Induced Hepatocellular Carcinoma Compared to Adjacent Liver Toxicol. Sci., December 1, 2005; 88(2): 319 - 330. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Li, Z. He, and J. Zhou Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation Nucleic Acids Res., October 24, 2005; 33(19): 6114 - 6123. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ning, K. P. Choi, H. W. Leong, and L. Zhang A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays Nucleic Acids Res., September 28, 2005; 33(17): e144 - e144. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Hyyro, M. Juhola, and M. Vihinen Genome-wide selection of unique and valid oligonucleotides Nucleic Acids Res., July 26, 2005; 33(13): e115 - e115. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Wernersson and H. B. Nielsen OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes Nucleic Acids Res., July 1, 2005; 33(suppl_2): W611 - W615. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Wu, R. Carta, and L. Zhang Sequence dependence of cross-hybridization on short oligo microarrays Nucleic Acids Res., May 24, 2005; 33(9): e84 - e84. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Nesvold, A. B. Kristoffersen, A. Holst-Jensen, and K. G. Berdal Design of a DNA chip for detection of unknown genetically modified organisms (GMOs) Bioinformatics, May 1, 2005; 21(9): 1917 - 1926. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Yamada and S. Morishita Accelerated off-target search algorithm for siRNA Bioinformatics, April 15, 2005; 21(8): 1316 - 1324. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. K. Nordberg YODA: selecting signature oligonucleotides Bioinformatics, April 15, 2005; 21(8): 1365 - 1370. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Rimour, D. Hill, C. Militon, and P. Peyret GoArrays: highly dynamic and efficient microarray probe design Bioinformatics, April 1, 2005; 21(7): 1094 - 1103. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Halperin, A. Buhot, and E. B. Zhulina Hybridization Isotherms of DNA Microarrays and the Quantification of Mutation Studies Clin. Chem., December 1, 2004; 50(12): 2254 - 2262. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. N. Messina, J. Glasscock, W. Gish, and M. Lovett An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression Genome Res., October 1, 2004; 14(10b): 2041 - 2047. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Hilson, J. Allemeersch, T. Altmann, S. Aubourg, A. Avon, J. Beynon, R. P. Bhalerao, F. Bitton, M. Caboche, B. Cannoot, et al. Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications Genome Res., October 1, 2004; 14(10b): 2176 - 2189. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. M. K. Gordon and C. W. Sensen Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays Nucleic Acids Res., September 29, 2004; 32(17): e133 - e133. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-C. Chou, C.-H. Chen, T.-T. Lee, and K. Peck Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression Nucleic Acids Res., July 8, 2004; 32(12): e99 - e99. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Halperin, A. Buhot, and E.B. Zhulina Sensitivity, Specificity, and the Hybridization Isotherms of DNA Chips Biophys. J., February 1, 2004; 86(2): 718 - 730. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Wang and B. Seed A PCR primer bank for quantitative gene expression analysis Nucleic Acids Res., December 15, 2003; 31(24): e154 - e154. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Haas, M. Hild, A. P. H. Wright, T. Hain, D. Talibi, and M. Vingron Genome-scale design of PCR primers and long oligomers for DNA microarrays Nucleic Acids Res., October 1, 2003; 31(19): 5576 - 5581. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Healy, E. E. Thomas, J. T. Schwartz, and M. Wigler Annotating Large Genomes With Exact Word Matches Genome Res., October 1, 2003; 13(10): 2306 - 2315. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Mei, E. Hubbell, S. Bekiranov, M. Mittmann, F. C. Christians, M.-M. Shen, G. Lu, J. Fang, W.-M. Liu, T. Ryder, et al. Probe selection for high-density oligonucleotide arrays PNAS, September 30, 2003; 100(20): 11237 - 11242. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Andronescu, R. Aguirre-Hernandez, A. Condon, and H. H. Hoos RNAsoft: a suite of RNA secondary structure prediction and design software tools Nucleic Acids Res., July 1, 2003; 31(13): 3416 - 3422. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. B. Nielsen, R. Wernersson, and S. Knudsen Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays Nucleic Acids Res., July 1, 2003; 31(13): 3491 - 3496. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. J. Emrich, M. Lowe, and A. L. Delcher PROBEmer: a web-based software tool for selecting optimal DNA oligos Nucleic Acids Res., July 1, 2003; 31(13): 3746 - 3750. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Tolstrup, P. S. Nielsen, J. G. Kolberg, A. M. Frankel, H. Vissing, and S. Kauppinen OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling Nucleic Acids Res., July 1, 2003; 31(13): 3758 - 3762. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Barczak, M. W. Rodriguez, K. Hanspers, L. L. Koth, Y. C. Tai, B. M. Bolstad, T. P. Speed, and D. J. Erle Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis Genome Res., July 1, 2003; 13(7): 1775 - 1785. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-M. Rouillard, M. Zuker, and E. Gulari OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach Nucleic Acids Res., June 15, 2003; 31(12): 3057 - 3062. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Bhanot, Y. Louzoun, J. Zhu, and C. DeLisi The Importance of Thermodynamic Equilibrium for High Throughput Gene Expression Arrays Biophys. J., January 1, 2003; 84(1): 124 - 135. [Abstract] [Full Text] [PDF]
|
|