Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
J Mol Biol. 2021 May 28;433(11):166860. doi: 10.1016/j.jmb.2021.166860. Epub 2021 Feb 2.
As a key region, promoter plays a key role in transcription regulation. A eukaryotic promoter database called EPD has been constructed to store eukaryotic POL II promoters. Although there are some promoter databases for specific prokaryotic species or specific promoter type, such as RegulonDB for Escherichia coli K-12, DBTBS for Bacillus subtilis and Pro54DB for sigma 54 promoter, because of the diversity of prokaryotes and the development of sequencing technology, huge amounts of prokaryotic promoters are scattered in numerous published articles, which is inconvenient for researchers to explore the process of gene regulation in prokaryotes. In this study, we constructed a Prokaryotic Promoter Database (PPD), which records the experimentally validated promoters in prokaryotes, from published articles. Up to now, PPD has stored 129,148 promoters across 63 prokaryotic species manually extracted from published papers. We provided a friendly interface for users to browse, search, blast, visualize, submit and download data. The PPD will provide relatively comprehensive resources of prokaryotic promoter for the study of prokaryotic gene transcription. The PPD is freely available and easy accessed at http://lin-group.cn/database/ppd/.
作为一个关键区域，启动子在转录调控中起着关键作用。已经构建了一个称为 EPD 的真核启动子数据库，用于存储真核 POL II 启动子。尽管有一些针对特定原核物种或特定启动子类型的启动子数据库，例如用于大肠杆菌 K-12 的 RegulonDB、用于枯草芽孢杆菌的 DBTBS 和用于 sigma 54 启动子的 Pro54DB，但由于原核生物的多样性和测序技术的发展，大量的原核启动子分散在众多已发表的文章中，这使得研究人员难以探索原核生物中的基因调控过程。在这项研究中，我们从已发表的文章中构建了一个原核启动子数据库（PPD），用于记录原核生物中经过实验验证的启动子。截至目前，PPD 已经手动从已发表的论文中提取了 63 个原核物种的 129148 个启动子。我们为用户提供了一个友好的界面，用于浏览、搜索、比对、可视化、提交和下载数据。PPD 将为原核生物基因转录的研究提供相对全面的原核启动子资源。PPD 可免费获取，并可在 http://lin-group.cn/database/ppd/ 轻松访问。
