Primer3_masker：将模板序列的屏蔽与引物设计软件相结合。
Primer3_masker: integrating masking of template sequence with primer design software.
机构信息
Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
出版信息
Bioinformatics. 2018 Jun 1;34(11):1937-1938. doi: 10.1093/bioinformatics/bty036.
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
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
设计用于扩增真核基因组区域的 PCR 引物是一项复杂的任务，因为基因组中包含大量的重复序列和其他不适合 PCR 扩增的区域。我们开发了一种新的基于 k-mer 的屏蔽方法，该方法使用统计模型在引物设计之前检测和屏蔽 DNA 模板上易出错的区域。我们将该软件实现为一个独立的软件 primer3_masker，并将其集成到引物设计程序 Primer3 中。
可用性和实现
primer3_masker 的独立版本是用 C 语言实现的。源代码可在以下网址免费获取：https://github.com/bioinfo-ut/primer3_masker/（适用于 Linux 和 macOS 的独立版本）和 https://github.com/primer3-org/primer3/（集成版本）。允许屏蔽 196 种动植物基因组序列的 Primer3 web 应用程序可在 http://primer3.ut.ee/ 上获得。
联系人
补充信息
补充数据可在 Bioinformatics 在线获取。
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