PreOpDB

PreOpDB predicts operon structures across more than 1200 prokaryotic genomes and provides searchable operon annotations to support analyses of genome organization, regulation, and metabolic pathway associations.

Key Features:

• Coverage: Operon predictions available for more than 1200 prokaryotic genomes.
• Operon Prediction Algorithm: Uses a novel operon identification algorithm to generate high-accuracy operonic structure predictions.
• Retrieval Options: Allows retrieval of operon predictions by organism name, KEGG metabolic pathways, COG orthology, Pfam conserved domains, or specific reference genes and operons.
• Non-Redundant Organism Selection: Selects non-redundant representative organisms using a precompiled phylogenetic distances matrix.
• Integration with Gene Context Tool: Provides operon predictions as input to the Gene Context Tool for visualization of genomic context and retrieval of 5' regulatory regions and nucleotide or amino acid sequences.

Scientific Applications:

• Genomic Research: Characterizing operon organization and regulatory relationships within prokaryotic genomes.
• Metabolic Engineering: Identifying operons involved in specific KEGG-defined metabolic pathways for biotechnological applications.
• Comparative Genomics: Enabling cross-species comparisons using COG orthology and Pfam conserved domain annotations.

Methodology:

Operon prediction is performed using a novel operon identification algorithm; operon sets can be filtered using KEGG, COG, and Pfam annotations; non-redundant organisms are selected via a precompiled phylogenetic distances matrix; operon outputs serve as input to the Gene Context Tool for retrieval of 5' regulatory regions and nucleotide or amino acid sequences.