Software for Multiplex Primer Design


This study presents a novel application, MultiPrimer, to assist users to design multiplex PCR primers. MultiPrimer adopts an algorithm based on a genetic algorithm and can efficiently solve the multi-objective optimisation problem. A match pattern model is proposed to speed up examination of the specificity constraint. MultiPrimer is able to find a set of primer pairs simultaneously for a set of gene family sequences and multiple targets for a single cDNA sequence. A public version of the MultiPrimer software is available from

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We thank Mr Chien-Chang Wu for valuable disucussions. We also thank for Mr Yuan-Ping Lin for performing the PCR experiments.

The authors have no conflicts of interest that are directly relevant to the content of this article.

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Correspondence to Prof. Chungnan Lee.

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Lee, C., Wu, J., Shiue, Y. et al. MultiPrimer. Appl-Bioinformatics 5, 99–109 (2006).

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  • Prime Pair
  • Multiplex Polymerase Chain Reaction
  • Specificity Constraint
  • Template Sequence
  • Polymerase Chain Reaction Experiment