MFEprimer-3.0: quality control for PCR primers
MFEprimer-3.0: quality control for PCR primers
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MFEprimer-3.0：PCR引物的质量控制
DOI：
10.1093/nar/gkz351
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发表时间：
2019-07-02
影响因子：
14.9
通讯作者：
Qu, Wubin
中科院分区：
文献类型：
--
作者：
Wang, Kun;Li, Haiwei;Qu, Wubin
摘要实验室设计的引物的质量控制是聚合酶链式反应(PCR)成功的关键。在这里，我们介绍了MFEprimer-3.0，这是一个用于检查非特异性扩增、二聚体、发夹和其他参数的功能性引物质量控制程序。当前版本的新特征包括：(I)使用更新的k-mer算法进行更敏感的结合位点搜索，该算法允许k-mer内的错配，但3‘端的第一个碱基除外。每一条具有稳定3‘端的引物的结合位点列在输出中；(Ii)快速鉴定自二聚体、交叉二聚体和发夹的新算法；(Iii)命令行版本，它增加了JSON输出选项，通过作为“Primer Design→Quality Control→ReDesign”管道中的QC步骤来增强MFEprimer的通用性；(Iv)检查结合位点是否包含单核苷酸多态(SNP)的功能，这将影响不同样本之间结合效率的一致性。综上所述，MFEprimer-3.0使用经过良好测试的PCR引物QC程序进行了更新，它可以作为QC模块集成到各种PCR引物设计应用程序中。无需登录即可免费访问MFEprimer-3.0服务器：https://mfeprimer3.igenetech.com/和https://www.mfeprimer.com/.命令行版本的源代码可根据要求提供。
Abstract Quality control (QC) for lab-designed primers is crucial for the success of a polymerase chain reaction (PCR). Here, we present MFEprimer-3.0, a functional primer quality control program for checking non-specific amplicons, dimers, hairpins and other parameters. The new features of the current version include: (i) more sensitive binding site search using the updated k-mer algorithm that allows mismatches within the k-mer, except for the first base at the 3′ end. The binding sites of each primer with a stable 3′ end are listed in the output; (ii) new algorithms for rapidly identifying self-dimers, cross-dimers and hairpins; (iii) the command-line version, which has an added option of JSON output to enhance the versatility of MFEprimer by acting as a QC step in the ‘primer design → quality control → redesign’ pipeline; (iv) a function for checking whether the binding sites contain single nucleotide polymorphisms (SNPs), which will affect the consistency of binding efficiency among different samples. In summary, MFEprimer-3.0 is updated with the well-tested PCR primer QC program and it can be integrated into various PCR primer design applications as a QC module. The MFEprimer-3.0 server is freely accessible without any login requirement at: https://mfeprimer3.igenetech.com/ and https://www.mfeprimer.com/. The source code for the command-line version is available upon request.