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A tool for high-throughput single nucleotide polymorphism (SNP) genotyping. It simulates a PCR and then compares in vitro and in silico PCR results. The tool reports amplimers close to or adjoining genes, SNPs, simple sequence repeats, and those that are shared between in vitro and in silico PCR results for selection of the most appropriate amplimers. It also compares physical and genetic maps to report the primer set genome coverage for PCR-walking.


Biology, Genetics, DNA polymorphism


  • Operation: Nucleic acid analysis, Genotyping
  • Software interface: Desktop graphical user interface
  • Language: C, Perl
  • Operating system: Linux, Microsoft Windows
  • License: Open source
  • Cost: Free
  • Version name: -
  • Credit: Alsamman MA, Ibrahim SD, Hamwieh A.
  • Contact: Dr. Shafik D. Ibrahim shaikdarwish at
  • Collection: -


Alsamman AM, Ibrahim SD, Hamwieh A "KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping." Bioinformatics 2019; 35(17):3187-3190
PMID: 30624621
PMCID: PMC6735863

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