Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
Nucleic Acids Res. 2021 Jan 8;49(D1):D229-D235. doi: 10.1093/nar/gkaa721.
T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.
T 盒核糖体开关构成了一大类 tRNA 结合的前导序列，在许多革兰氏阳性菌的基因调控中发挥着核心作用。准确推断 T 盒核糖体开关与 tRNA 的结合对于预测其顺式调控活性至关重要。然而，目前还没有关于 T 盒核糖体开关与 tRNA 结合特异性的中央信息库，并且从头预测结合特异性需要先进的计算工具知识来注释核糖体开关二级结构特征。在这里，我们介绍了 T 盒核糖体开关注释数据库（TBDB，https://tbdb.io），这是一个开放获取的数据库，其中包含了 23535 个 T 盒核糖体开关序列，涵盖了 3632 个细菌物种的主要门。在结构预测中，TBDB 还可以识别指定序列、同源 tRNA 结合伙伴和下游调控靶标。据我们所知，TBDB 提供了关于这个重要的调控 RNA 家族的最大特征、序列和结构注释集合。
