RegPrecise

RegPrecise catalogs predicted transcription factor regulons in prokaryotic genomes to support reconstruction, comparative analysis, and manual curation of transcriptional regulatory networks.

Key Features:

• Comparative Genomics Approach: Uses comparative genomics to predict transcriptional regulatory interactions and infer transcription factor binding motifs across prokaryotic genomes.
• Regulon Visualization and Analysis: Provides analyses of conservation patterns of DNA binding sites and regulated genes, sets of regulons by transcription factor families, regulon repertoires across taxa, and links between regulons and metabolic pathways or biological processes.
• Extensive Data Coverage: Contains over 11,500 candidate binding sites for approximately 400 orthologous transcription factor groups from more than 350 prokaryotic genomes, including genome-wide reconstructions in Shewanella and Streptococcus and large-scale predictions for the LacI family.
• Regulog Reconstruction: Captures regulogs—sets of genes regulated by orthologous regulators across related genomes—for comparative reconstruction of regulatory interactions.
• API Access: Includes a Web Services API with 14 web service resources for programmatic querying and data retrieval, and RegPrecise 2.0 comprises over 1,400 regulogs from more than 250 genomes across 24 taxonomic groups.

Scientific Applications:

• Automatic Annotation: Provides reference regulons to support automated annotation of regulatory interactions in newly sequenced genomes.
• Comparative Studies: Enables comparative analyses of transcriptional regulation across bacterial species and taxonomic groups.
• Pathway Analysis: Facilitates exploration of regulons associated with metabolic pathways and biological processes to interpret microbial physiology and adaptation.

Methodology:

Comparative genomics-based prediction of transcription factor binding sites and reconstruction of regulons, combined with manual curation.