Primer3_masker: integrating masking of template sequence with primer design software.

Autor: Kõressaar T; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia., Lepamets M; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia., Kaplinski L; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia., Raime K; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia., Andreson R; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia., Remm M; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
Jazyk: angličtina
Zdroj: Bioinformatics (Oxford, England) [Bioinformatics] 2018 Jun 01; Vol. 34 (11), pp. 1937-1938.
DOI: 10.1093/bioinformatics/bty036
Abstrakt: 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.
Databáze: MEDLINE
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