Primer3_masker: integrating masking of template sequence with primer design software | Zendy

Triinu Kõressaar | Zendy; Maarja Lepamets | Zendy; Lauris Kaplinski | Zendy; Kairi Raime | Zendy; Reidar Andreson | Zendy; Maido Remm | Zendy

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Primer3_masker: integrating masking of template sequence with primer design software

Author(s) -

Triinu Kõressaar,

Maarja Lepamets,

Lauris Kaplinski,

Kairi Raime,

Reidar Andreson,

Maido Remm

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty036

Subject(s) - primer (cosmetics) , masking (illustration) , software , computer science , source code , genome , code (set theory) , computational biology , biology , programming language , genetics , art , chemistry , organic chemistry , set (abstract data type) , visual arts , gene

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.

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