PT  - JOURNAL ARTICLE
AU  - Jorge A. Marchand
AU  - Merrick D. Pierson Smela
AU  - Thomas H. H. Jordan
AU  - Kamesh Narasimhan
AU  - George M. Church
TI  - TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs
AID  - 10.1101/2020.06.17.157016
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.17.157016
4099  - http://biorxiv.org/content/early/2020/06/19/2020.06.17.157016.short
4100  - http://biorxiv.org/content/early/2020/06/19/2020.06.17.157016.full
AB  - 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-boxes 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 advance knowledge of computational tools to annotate riboswitch secondary structure features. Here we present T-box annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,497 T-box sequences, spanning the major phyla of 3,621 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory target. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.Competing Interest StatementThis project has been funded by DOE grant DE-FG02-02ER63445. Dr. Church is a founder of the following companies in which he has related financial interests: ReadCoor; EnEvolv; and 64-x. For a complete list of financial interests of Prof. George Church, see also http://arep [dot]med[dot]harvard[dot]edu/gmc/tech[dot]html