RExPrimer is an integrated web-based application for primer design which includes the following features :

  • Primer design for PCR/resequencing and SNP genotyping which covers both gene and non-gene target regions in human genome.
  • Notification of SNP-in-Primer destabilizing effect based on common and population-specific SNP data retrieved from various databases
    (NCBI dbSNP build 129, HapMap public release 27, JSNP release 35, and ThaiSNP release 2).
  • Avoiding possible mis-priming due to target related sequences by crosschecking target sequence against locally constructed pseudogene database
    retrieved from
  • Reporting structural polymorphisms which potentially cause PCR failure by checking target sequence with genomic variation databases covering
    Copy Number Variations (CNVs) and indel polymorphisms (data from Database of Genomic Variant).
  • Primer redesign module that allows users to specify the desired primer location and primer condition.
  • Uniqueness test of resulting primer sequences by In-Silico PCR provided as the links from the output report.
  • Interactive graphical visualization with Scalable Vector Graphics (SVG) displaying designed primer pairs with corresponding genomic features.
  • Oligonucleotide checking module for verifying the specificity of input primer sequence as well as determining the primer product and condition.


  • Piriyapongsa J, Ngamphiw C, Assawamakin A, Wangkumhang P, Suwannasri P, Ruangrit U, Agavatpanitch G and Tongsima S.
    RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.
    BMC Genomics 2009, 10(Suppl 3):S4.

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