MultiPrimer: A System for Microarray PCR Primer Design

To construct full-genome spotted microarrays, a large number ofPCR primers that amplify the required DNA need to be synthesized.We describe an algorithmic technique that allows one to use fewerprimers to achieve this goal. This can reduce the expense of primers are usually designed, so that each primer occurs uniquely in the genome. This condition is unnecessarily strong for selective amplification, because only the primer pair associated with each amplification needs be unique. We also describe the interface to our software, MultiPrimer, that computes a small set of primers for amplification of a given gene set.