PRIMEGENSw3: a web-based tool for high-throughput primer and probe design.
PRIMEGENSw3: a web-based tool for high-throughput primer and probe design.
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DOI：
10.1007/978-1-4939-2365-6_14
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发表时间：
2015-01-01
期刊：
影响因子：
--
通讯作者：
Xu, Dong
中科院分区：
文献类型：
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作者：
Kushwaha, Garima;Srivastava, Gyan Prakash;Xu, Dong
高特异性和高效率的引物和探针设计一直是许多高通量技术的主要障碍。任何聚合酶链式反应或探针杂交技术的成功实施取决于所使用的引物和探针的特异性和交叉杂交的质量。在这里，我们描述了PRIMEGENSw3，这是一组基于网络的实用程序，用于高通量引物和探针设计。这些实用程序允许用户选择基因组区域，并以交互、用户友好和自动的方式为所选区域设计引物/探针。系统在高性能服务器的后端运行PRIMEGENS算法，存储基因组数据库或用户提供的定制数据库用于杂交检查。杂交不仅使用BLAST进行检查，还通过检查错配位置和潜在杂交命中的能量计算来进行检查。结果可以在网上可视化，也可以下载。用PRIMEGENSw3设计引物的平均成功率为90%。该网络服务器还支持用于表观遗传学研究的甲基化序列的引物设计。该软件的单机版也可在网站上下载。
Highly specific and efficient primer and probe design has been a major hurdle in many high-throughput techniques. Successful implementation of any PCR or probe hybridization technique depends on the quality of primers and probes used in terms of their specificity and cross-hybridization. Here we describe PRIMEGENSw3, a set of web-based utilities for high-throughput primer and probe design. These utilities allow users to select genomic regions and to design primer/probe for selected regions in an interactive, user-friendly, and automatic fashion. The system runs the PRIMEGENS algorithm in the back-end on the high-performance server with the stored genomic database or user-provided custom database for cross-hybridization check. Cross-hybridization is checked not only using BLAST but also by checking mismatch positions and energy calculation of potential hybridization hits. The results can be visualized online and also can be downloaded. The average success rate of primer design using PRIMEGENSw3 is ~90 %. The web server also supports primer design for methylated sequences, which is used in epigenetic studies. Stand-alone version of the software is also available for download at the website.