Probe design for expression arrays using OligoWiz.

Abstract

Since all measurements from a DNA microarray is dependant on the probes used, a good choice of probes is of vital importance when designing custom microarrays. This chapter describes how to design expression arrays using the OligoWiz software suite. The desired general features of good probes and the issues which probe design must address are introduced and a conceptual (rather than mathematical) description of how OligoWiz scores the quality of the potential probes is presented. This is followed by a detailed step-by-step guide to designing expression arrays with OligoWiz.The scope of this chapter is exclusively on expression arrays. For an in-depth review of the entire field of probe design (including a comparison of different probe design packages) as well as instructions on how to produce special purpose arrays (e.g., splice detection arrays), please refer to (1).