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Probe selection for DNA microarrays using OligoWiz

Nature Protocols volume 2, pages 2677–2691 (2007)Cite this article

Abstract

Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client–server application that offers a detailed graphical interface and real-time user interaction on the client side, and massive computer power and a large collection of species databases (400, summer 2007) on the server side. Probes are selected according to five weighted scores: cross-hybridization, ΔTm, folding, position and low-complexity; and probes can be placed with respect to sequence annotation using regular expressions. This protocol provides recommendations related to the design and parameter settings, and it also offers a comprehensive walkthrough of the design steps. The protocol requires limited computer skills and can be executed from any Internet-connected computer. The probe selection procedure for a standard microarray design targeting all yeast transcripts can be completed in 1 h.

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Figure 1: CLN2 profile.
Figure 2: Signal intensity decrease for degenerated short oligonucleotides.
Figure 3: Launching a query.
Figure 4: Main probe selection/inspection interface.
Figure 5: Usage of the species databases.
Figure 6: Avoiding regions with high similarity to other transcripts.
Figure 7: Tm distribution in optimized length intervals of oligonucleotides.
Figure 8: The five position scores in OligoWiz 2.0.
Figure 9
Figure 10: Visualization of the principles behind the probe placement filters in OligoWiz.
Figure 11: Experimental validation of probe quality.

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Authors and Affiliations

  1. Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, 2800, Denmark

    Rasmus Wernersson, Agnieszka S Juncker & Henrik Bjørn Nielsen

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  1. Rasmus Wernersson
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Correspondence to Rasmus Wernersson.

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Wernersson, R., Juncker, A. & Nielsen, H. Probe selection for DNA microarrays using OligoWiz. Nat Protoc 2, 2677–2691 (2007). https://doi.org/10.1038/nprot.2007.370

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