Multiplex primer prediction software for divergent targets

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

The MPP algorithm described here focuses on finding conserved primers, and does not require that the primers be family-or species-specific. For the runs predicting family-specific primers, we designed viral family primers that were unique relative to nontarget viral families by replacing any substring of 17 nt or longer that occurs in any non-target family with a substring of 'N''s, using the suffix array software vmatch (http://www.vmatch.de/). MPP eliminates oligos with N's from consideration as primers. This approach is simple, although it risks being overly strict by eliminating some potentially successful candidate primers, since it disallows those cases where a single nonunique primer pairs with a unique primer, a pair of nonunique primers are too far apart to actually generate an amplicon in a nontarget sequence, or candidate oligos partially overlap a nonunique stretch of N's.