Li Xiaodong, Meng Boyu, Zhang Zhi, Wei Lijuan, Chang Wei, Wang Yuhong, Zhang Kai, Li Tian, Lu Kun
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, China.
Nucleic Acids Res. 2025 Jan 6;53(D1):D205-D210. doi: 10.1093/nar/gkae684.
High-quality primer design is essential for the success of all polymerase chain reaction (PCR)-based experiments. We previously developed a thermodynamics-based gene-specific quantitative PCR (qPCR) primer database for 147 organisms, which has been used extensively in gene expression studies. However, the number of organisms and the imperfection of function in the database limits its potential applications. Here, we improved the functionality of qPrimerDB to create a more comprehensive primer resource. Specifically, we (i) developed an improved primer design tool, qPrimer, building upon the previous qPrimerDB pipeline, to enhance the efficiency and simplicity of genome-scale qPCR primer design; (ii) pre-computed qPCR primer resources from 1 308 genomes of 1172 organisms and (iii) introduced a complete system for identifying, designing, checking, marking, and submitting qPCR primers. qPrimerDB 2.0 is freely available at https://qprimerdb.biodb.org. The qPrimer source code is available at https://github.com/swu1019lab/qPrimer.
高质量的引物设计对于所有基于聚合酶链反应（PCR）的实验的成功至关重要。我们之前为147种生物开发了一个基于热力学的基因特异性定量PCR（qPCR）引物数据库，该数据库已在基因表达研究中广泛使用。然而，数据库中生物的数量以及功能的不完善限制了其潜在应用。在此，我们改进了qPrimerDB的功能，以创建一个更全面的引物资源。具体而言，我们（i）在之前的qPrimerDB流程基础上开发了一种改进的引物设计工具qPrimer，以提高基因组规模qPCR引物设计的效率和简便性；（ii）从1172种生物的1308个基因组中预先计算了qPCR引物资源，以及（iii）引入了一个用于识别、设计、检查、标记和提交qPCR引物的完整系统。qPrimerDB 2.0可在https://qprimerdb.biodb.org免费获取。qPrimer的源代码可在https://github.com/swu1019lab/qPrimer获取。
