Primer3_masker: integrating masking of template sequence with primer design software

Bioinformatics. 2018 Jun 1;34(11):1937-1938. doi: 10.1093/bioinformatics/bty036.


Summary: Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3.

Availability and implementation: The standalone version of primer3_masker is implemented in C. The source code is freely available at (standalone version for Linux and macOS) and at (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA Primers*
  • Humans
  • Plants / genetics
  • Polymerase Chain Reaction / methods*
  • Repetitive Sequences, Nucleic Acid*
  • Software*


  • DNA Primers