TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci
TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci
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TADB 2.0：细菌 II 型毒素-抗毒素基因座的更新数据库
DOI：
10.1093/nar/gkx1033
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Ou, Hong-Yu
中科院分区：
文献类型：
--
作者：
Xie, Yingzhou;Wei, Yiqing;Ou, Hong-Yu
TADB2.0(http://bioinfo-mml.sjtu.edu.cn/TADB2/)是一个更新的数据库，提供有关细菌II型毒素-抗毒素(TA)基因座的全面信息。与前一版本相比，改进了数据库，采用了新的数据模式。借助于文本挖掘和人工筛选，在细菌和古菌的870个复制子中记录了6193个II型TA基因座，其中包括105个实验验证的TA基因座。此外，新开发的工具TAfinder结合了同源搜索和操纵子结构检测，允许预测细菌基因组序列中的II型TA对。它还有助于通过与特定公共数据库的比对来调查推测的毒力因子、抗菌素耐药决定因素和移动遗传元件的预测TA基因座的基因组背景。此外，模块TAfinder-Compare允许比较近亲基因组中给定TA基因座的存在。随着最近的更新，TADB2.0可能会为理解II型TA系统在原核生物生命活动中的重要作用提供更好的支持。
TADB2.0 (http://bioinfo-mml.sjtu.edu.cn/TADB2/) is an updated database that provides comprehensive information about bacterial type II toxin-antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences. It also helps to investigate the genomic context of predicted TA loci for putative virulence factors, antimicrobial resistance determinants and mobile genetic elements via alignments to the specific public databases. Additionally, the module TAfinder-Compare allows comparing the presence of the given TA loci across the close relative genomes. With the recent updates, TADB2.0 might provide better support for understanding the important roles of type II TA systems in the prokaryotic life activities.