Multiplex primer prediction software for divergent targets

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

We evaluated how the growth of sequence availability could affect the size of the universal set of viral primers, as well as our ability to detect unknown/unsequenced viruses. We predicted a universal viral primer set for all viral genomes and segments available as of 1 January 2004, totaling 9965 sequences, for primers of length 7-15 nt ( Figure 2 ). It was not necessary to exclude any Orthomyxoviridae or Bunyaviridae segments, because these segments were not so deeply sequenced at that time. We then determined how much of the 2007 sequence data would have been detectable using the 2004 primer sets (Figure 3 ).