MultiPLX: Automatic Grouping and Evaluation of PCR Primers

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-defined compatibility level. In addition, it can be used to select optimal primer pairs for multiplexing from list of candidates. MultiPLX can be downloaded from http://bioinfo.ut.ee/download/ . Graphical Web-based interface to most functions of MultiPLX is available at http://bioinfo.ut.ee/multiplx/ .