An iterative method for selecting degenerate multiplex PCR primers

Richard Souvenir, Jeremy Buhler, Gary Stormo, Weixiong Zhang

Research output: Chapter in Book/Report/Conference proceedingChapter

9 Scopus citations


Single-nucleotide polymorphism (SNP) genotyping is an important molecular genetics process, which can produce results that will be useful in the medical field. Because of inherent complexities in DNA manipulation and analysis, many different methods have been proposed for a standard assay. One of the proposed techniques for performing SNP genotyping requires amplifying regions of DNA surrounding a large number of SNP loci. To automate a portion of this particular method, it is necessary to select a set of primers for the experiment. Selecting these primers can be formulated as the Multiple Degenerate Primer Design (MDPD) problem. The Multiple, Iterative Primer Selector (MIPS) is an iterative beam-search algorithm for MDPD. Theoretical and experimental analyses show that this algorithm performs well compared with the limits of degenerate primer design. Furthermore, MIPS outperforms an existing algorithm that was designed for a related degenerate primer selection problem.

Original languageEnglish
Title of host publicationPCR Primer Design
EditorsAnton Yuryev
Number of pages23
StatePublished - Aug 2 2007
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Degenerate primers
  • Multiplex PCR
  • SNP genotyping

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  • Cite this

    Souvenir, R., Buhler, J., Stormo, G., & Zhang, W. (2007). An iterative method for selecting degenerate multiplex PCR primers. In A. Yuryev (Ed.), PCR Primer Design (pp. 245-267). (Methods in Molecular Biology; Vol. 402).