MultiPLX: Automatic Grouping and Evaluation of PCR Primers

  • Lauris Kaplinski
  • Maido RemmEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1275)


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 Graphical web-based interface to most functions of MultiPLX is available at

Key words

PCR Multiplex Primer design 



This work was supported by the grant EU19730 from Enterprise Estonia. Development of primer design software in our group has been funded by Centre of Excellence in Genomics at Estonian Biocentre (EU European Regional Development Fund). The authors thank Katre Palm for a valuable help with English grammar.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of BioinformaticsUniversity of TartuTartuEstonia
  2. 2.Estonian BiocentreTartuEstonia

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