Probe Selection for DNA Microarrays using OligoWiz

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.