ODB

ODB compiles comprehensive data on known and conserved operons across completely sequenced genomes to support analysis and prediction of gene regulation and operonic structures.

Key Features:

• Extensive Operon Data Collection: The database contains information on approximately 10,000 known operons from over 50 genomes and more than 400,000 conserved operons derived from over 1,000 bacterial genomes.
• Integration of High-Throughput Transcriptional Unit Data: ODB incorporates genome-wide transcriptional unit data from high-throughput analyses in five prokaryotic and two eukaryotic organisms.
• Reference Operons for Operon Prediction: Known operons are clustered to define reference operons that identify sets of possible orthologous genes organizing operonic structures for predictive modeling.

Scientific Applications:

• Gene regulation and expression analysis: Use of curated operon and transcriptional unit data to study coordinated gene expression and regulatory organization.
• Operon prediction: Application of reference operons and clustering-derived orthology sets to predict operonic structures in new genomes.
• Comparative genomics: Comparison of conserved operons across over 1,000 bacterial genomes to investigate conservation and variation of gene organization.
• Evolutionary biology: Analysis of operon conservation and orthologous gene sets to infer evolutionary relationships and operon evolution.
• Functional genomics: Integration of operon and transcriptional unit data to support functional assignment and pathway-level interpretation of gene clusters.

Methodology:

Systematic collection and curation of operon data from completely sequenced genomes; clustering of known operons to define reference operons and identify possible orthologous gene sets; integration of genome-wide transcriptional unit analyses.