Primer design for multiplex PCR using a genetic algorithm

Li Cheng Wu, Jorng Tzong Horng, Hsi Yuan Huang, Feng Mao Lin, Hsien Da Huang, Meng Feng Tsai

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Multiplex Polymerase chain reaction (PCR) is the term used when more than one pair of primers is used in a polymerase chain reaction. The goal of multiplex PCR is to amplify several segments of target DNA simultaneously and thereby to conserve template DNA, save time, and minimize expense. The success of the experiment is dependent on primer design. However, this can be a dreary task as there are many constrains such as melting temperatures, primer length, GC content and complementarity that need to be optimized to obtain a good PCR product. In our investigations, we found few primer design tools for multiplex PCR and there was no suitable tool for our partners who want to use a multiplex PCR genotypic assay. The tool draws on a genetic algorithm where stochastic approaches based on the concept of biological evolution, biological genetics and genetic operations on chromosomes are used to find an optimal solution for multiplex PCR. The presented experimental results indicate that the proposed algorithm is able to find a set of primer pairs that not only obey the design properties but also work in the same tube.

Original languageEnglish
Pages (from-to)855-863
Number of pages9
JournalSoft Computing
Issue number9
StatePublished - Jul 2007


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