How to create a microarray?
Probe design has to follow several principles to optimize their specificity and sensitivity: • Mask repeat patterns • Prevent sequence homology with other targets • Thermodynamic properties of all probes have to be in the same range (e.g. melting temperature) • Prevent self-hybridization and formation of internal secondary structures Luckily for you, all these subsequent steps are now automated for you and designing a microarray is very much a black-box process, where by you only have to specify your target sequences. Yet it is still important to understand the underlying principles to provide these software with the correct data. Most commercial vendors have their own Microarray design platform, e.g. Agilent or Affymetrix. However, third-party software, independent from any vendor is also available. Some software is available for free (such as Picky, developed here at Iowa State University; registration required) or commercial (such as Array Designer). In this course, we will use Pick
