Computational Methods for Probe Design and Selection
Abstract There is a direct correlation between the cost and efﬁciency of hybridization experiments and the quality of the probes used in the experiments. Many factors must be considered in designing and selecting probes for use in experiments and these factors are generally dictated by the
primary goals of the experiment. In this chapter, we focus on computational methods for the design and selection of probes. We consider properties of probes such as the melting temperature, speciﬁcity, existence of secondary structures, and probe length. We also discuss various algorithms and software packages that have been developed to aid in the design and selection of probes.