title: Probe selection for DNA microarrays using OligoWiz.
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.
authors.affiliation: Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby 2800, Denmark. raz@cbs.dtu.dk
authors.forename: Rasmus
authors.initials: R
authors.lastname: Wernersson
authors.forename: Agnieszka S
authors.initials: AS
authors.lastname: Juncker
authors.forename: Henrik Bjørn
authors.initials: HB
authors.lastname: Nielsen
mesh_terms: D016213:Cyclins / Q000737:chemistry / Q000235:genetics; D015342:DNA Probes / Q000737:chemistry*; D030541:Databases, Genetic; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D029701:Saccharomyces cerevisiae Proteins; D012984:Software
chemical_list: C082721:CLN2 protein, S cerevisiae; D016213:Cyclins; D015342:DNA Probes; D029701:Saccharomyces cerevisiae Proteins