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SCHOLARLY PUBLICATION ✓ Open Access

Primer3_masker: integrating masking of template sequence with primer design software

Triinu Kõressaar, Maarja Lepamets, Lauris Kaplinski, Kairi Raime, Reidar Andreson, Maido Remm

📖 Bioinformatics → 📅 2018-01-18 🔗 DOI: 10.1093/bioinformatics/bty036
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📄 Abstract

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 https://github.com/bioinfo-ut/primer3_masker/ (standalone version for Linux and macOS) and at https://github.com/primer3-org/primer3/ (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http://primer3.ut.ee/. Contact: maido.remm@ut.ee. Supplementary information: Supplementary data are available at Bioinformatics online.

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