GroovDB: A database of ligand-inducible transcription factors

Abstract

Genetic biosensors are integral to synthetic biology. In particular, ligand-inducible prokaryotic transcription factors are frequently used in high-throughput screening, for dynamic feedback regulation, as multi-layer logic gates, and in diagnostic applications. In order to provide a curated source that users can rely on for engineering applications, we have developed GroovDB (available at https://groov.bio), a Web-accessible database of ligand-inducible transcription factors that contains all information necessary to build chemically-responsive genetic circuits, including biosensor sequence, ligand, and operator data. Ligand and DNA interaction data has been verified against the literature, while an automated data curation pipeline is used to programmatically fetch metadata, structural information, and references for every entry. A custom tool to visualize the natural genetic context of biosensor entries provides additional information that provides potential insights into alternative ligands and systems biology.