Dudek Christian-Alexander, Jahn Dieter
Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany.
Nucleic Acids Res. 2022 Jan 7;50(D1):D295-D302. doi: 10.1093/nar/gkab1110.
PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.
PRODORIC是全球最大的来自多种细菌来源的原核转录因子结合位点集合之一,并配有相应的解释和可视化工具。随着2017年PRODORIC2的推出,开始向现代网络界面和可维护的后端过渡。随着PRODORIC的此次最新版本发布,数据库后端现在完全基于应用程序编程接口(API),并提供对完整PRODORIC数据的编程访问。最初PRODORIC中的可视化工具基因组浏览器(Genome Browser)和ProdoNet已重新引入并集成到PRODORIC网站中。针对基于位置权重矩阵模式的搜索,再次添加了原始虚拟足迹(Virtual Footprint)中缺失的输入和输出选项。整个PRODORIC数据集都重新进行了注释。对每个转录因子结合位点都重新进行了评估,以提高整体数据库质量。在此过程中,为每个转录因子添加了诸如结合效应物、调控类型和不同类型实验证据等额外参数。此外,还添加了109个新的转录因子和6个新的生物体。PRODORIC可在https://www.prodoric.de上公开获取。