PRODORIC

PRODORIC provides a curated database of prokaryotic transcription factor binding sites and associated regulatory annotations to support analysis of bacterial gene regulation.

Key Features:

• Extensive Data Collection: Contains one of the largest collections of prokaryotic transcription factor binding sites compiled from multiple bacterial organisms.
• API-based backend: Maintains an API-based backend for programmatic access to its dataset.
• Visualization Tools: Integrates visualization tools including Genome Browser and ProdoNet for exploration of transcription factor binding data.
• Position Weight Matrix Search: Supports position weight matrix pattern-based searches with restored input and output options from the Virtual Footprint tool.
• Reannotation and Quality Improvement: Re-evaluated and reannotated all binding sites, adding parameters such as bound effectors, regulation type, and types of experimental evidence.
• Expanded Content: Latest release includes 109 new transcription factors and six newly added organisms.

Scientific Applications:

• Identification of regulatory elements: Enables detection and cataloging of transcription factor binding sites across bacterial genomes.
• Prediction of gene function: Provides regulatory context to support inference of gene function from transcriptional regulation patterns.
• Evolutionary and comparative analyses: Facilitates exploration of regulatory relationships and conservation among bacterial species.

Methodology:

Rigorous re-evaluation and reannotation of transcription factor binding sites integrating multiple types of experimental evidence and annotating bound effectors and regulation types.