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

Bioinformatics 2018 06;34(11):1937-1938

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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.

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty036DOI Listing
June 2018
10 Reads

Publication Analysis

Top Keywords

primer design
12
standalone version
8
detect mask
4
application allows
4
model detect
4
mask failure-prone
4
failure-prone regions
4
template prior
4
prior primer
4
web application
4
dna template
4
regions dna
4
allows masking
4
statistical model
4
linux macos
4
196 animal
4
developed novel
4
pcr developed
4
k-mer based
4
based masking
4

Similar Publications