Probe Selection for DNA Microarrays using OligoWiz

Rasmus Wernersson, Agnieszka Juncker, Henrik Bjørn Nielsen

    Research output: Contribution to journalJournal articleResearchpeer-review

    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, deltaT(m), 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.
    Original languageEnglish
    JournalNature protocols
    Issue number11
    Pages (from-to)2677-91
    ISSN1754-2189
    DOIs
    Publication statusPublished - 2007

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