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Primer3_masker: integrating masking of template sequence with primer design software

2018; Oxford University Press; Volume: 34; Issue: 11 Linguagem: Inglês

10.1093/bioinformatics/bty036

1367-4811

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

Genetic diversity and population structure

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.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/.maido.remm@ut.ee.Supplementary data are available at Bioinformatics online.