State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.
Nucleic Acids Res. 2024 Jan 5;52(D1):D784-D790. doi: 10.1093/nar/gkad962.
TADB 3.0 (https://bioinfo-mml.sjtu.edu.cn/TADB3/) is an updated database that provides comprehensive information on bacterial types I to VIII toxin-antitoxin (TA) loci. Compared with the previous version, three major improvements are introduced: First, with the aid of text mining and manual curation, it records the details of 536 TA loci with experimental support, including 102, 403, 8, 14, 1, 1, 3 and 4 TA loci of types I to VIII, respectively; Second, by leveraging the upgraded TA prediction tool TAfinder 2.0 with a stringent strategy, TADB 3.0 collects 211 697 putative types I to VIII TA loci predicted in 34 789 completely sequenced prokaryotic genomes, providing researchers with a large-scale dataset for further follow-up analysis and characterization; Third, based on their genomic locations, relationships of 69 019 TA loci and 60 898 mobile genetic elements (MGEs) are visualized by interactive networks accessible through the user-friendly web page. With the recent updates, TADB 3.0 may provide improved in silico support for comprehending the biological roles of TA pairs in prokaryotes and their functional associations with MGEs.
TADB 3.0（https://bioinfo-mml.sjtu.edu.cn/TADB3/）是一个更新的数据库，提供了关于细菌类型 I 至 VIII 毒素-抗毒素（TA）基因座的全面信息。与之前的版本相比，引入了三个主要改进：首先，借助文本挖掘和人工注释，记录了 536 个具有实验支持的 TA 基因座的详细信息，包括类型 I 至 VIII 的 102、403、8、14、1、1、3 和 4 个 TA 基因座；其次，利用升级后的 TA 预测工具 TAfinder 2.0 采用严格的策略，TADB 3.0 收集了 34789 个完全测序的原核基因组中预测的 211697 个假定的类型 I 至 VIII TA 基因座，为研究人员提供了一个大规模数据集，用于进一步的后续分析和表征；第三，根据它们的基因组位置，通过用户友好的网页可访问的交互式网络可视化了 69019 个 TA 基因座和 60898 个移动遗传元件（MGE）之间的关系。随着最近的更新，TADB 3.0 可能会为理解 TA 对在原核生物中的生物学作用及其与 MGE 的功能关联提供改进的计算支持。
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