PRIMEval: Optimization and screening of multiplex oligonucleotide assays

Sci Rep. 2019 Dec 17;9(1):19286. doi: 10.1038/s41598-019-55883-4.


The development of multiplex polymerase chain reaction and microarray assays is challenging due to primer dimer formation, unspecific hybridization events, the generation of unspecific by-products, primer depletion, and thus lower amplification efficiencies. We have developed a software workflow with three underlying algorithms that differ in their use case and specificity, allowing the complete in silico evaluation of such assays on user-derived data sets. We experimentally evaluated the method for the prediction of oligonucleotide hybridization events including resulting products and probes, self-dimers, cross-dimers and hairpins at different experimental conditions. The developed method allows explaining the observed artefacts through in silico WGS data and thermodynamic predictions. PRIMEval is available publicly at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computer Simulation
  • DNA Primers / genetics
  • Multiplex Polymerase Chain Reaction / methods*
  • Nucleic Acid Hybridization / genetics*
  • Nucleic Acid Hybridization / methods
  • Oligonucleotide Probes / genetics
  • Oligonucleotides / genetics*
  • Sequence Analysis, DNA
  • Software*


  • DNA Primers
  • Oligonucleotide Probes
  • Oligonucleotides