TBDB

TBDB catalogs and annotates 23,497 T-box riboswitch sequences derived from 3,621 bacterial species across major phyla to provide sequence, secondary-structure, specifier, cognate tRNA partner, downstream regulatory target, and thermodynamic information for studying tRNA-dependent transcriptional regulation and tRNA-binding leader function in bacteria.

Key Features:

• Extensive Sequence Collection: Contains 23,497 T-box sequences derived from 3,621 bacterial species across major phyla.
• Structural Predictions: Provides secondary-structure annotations for T-box riboswitches.
• Specifier Sequences and tRNA Partners: Identifies specifier sequences within T-boxes and predicts cognate tRNA binding partners.
• Regulatory Target Identification: Annotates downstream regulatory targets associated with T-box riboswitches.
• Thermodynamic Calculations: Supplies thermodynamic calculations for putative T-box sequences to assess stability and functionality.

Scientific Applications:

• Functional Genomics: Enables analysis of the regulatory roles of T-box riboswitches in bacterial gene expression.
• Comparative Genomics: Supports comparative studies across bacterial phyla to examine conservation and evolutionary patterns of T-box elements.
• Structural Biology: Informs modeling of RNA secondary structure and RNA–tRNA interactions.
• Synthetic Biology: Provides sequence and structural data usable for designing synthetic riboswitches with defined regulatory properties.

Methodology:

Computational annotation including secondary-structure prediction, identification of specifier sequences, de novo prediction of cognate tRNA binding partners, and thermodynamic calculations.