Multiplex primer prediction software for divergent targets

Gardner, Shea N.; Hiddessen, Amy L.; Williams, Peter L.; Hara, Christine; Wagner, Mark C.; Colston, Bill W.

In addition to finding primers for viral detection, another application of MPP could be to design multiplex primers for homologs in a gene family. The user can specify an appropriate product length range to ensure amplification of an adequate span across the gene. MPP could also be used to design multiplex primer sets for unrelated target sequences, for example, multiple bacterial and viral species or gene families, in a single reaction. Since no sequence alignment is required, there is no need for any sequence conservation among targets. Recent work showed that a large-scale multiplex of 800 primer pairs specifically designed to detect a diverse set of genes from nine pathogens improved sensitivity on a microarray by up to 1000-fold (39) . The MPP software could be used to design multiplex primer sets for similar work.