MultiPLX: Automatic grouping and evaluation of PCR primers

Abstract

In this chapter we describe MultiPLX—a tool for automatic grouping of PCR primers for multiplexed PCR. Both generic working principle and step-by-step practical procedures with examples are presented. MultiPLX performs grouping by calculating many important interaction levels between the different primer pairs and then distributes primer pairs to groups so that the strength of unwanted interactions is kept below user-defi ned compatibility level. In addition it can be used to select optimal primer pairs for multiplexing from list of candidates.