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ODB: a database for operon organizations, 2011 update.

Shujiro Okuda1, Akiyasu C Yoshizawa

  • 1College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan. okd@sk.ritsumei.ac.jp

Nucleic Acids Research
|November 6, 2010
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Summary
This summary is machine-generated.

The Operon DataBase (ODB) now integrates updated operon data, including genome-wide analyses, and introduces "reference operons" for improved prediction. New graphical interfaces facilitate comparative and visualization analyses of operon structures across multiple genomes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The Operon DataBase (ODB) is a comprehensive resource for known and conserved operons in sequenced genomes.
  • Genome-wide analyses of transcription and transcriptional units are increasingly important in biological research.

Purpose of the Study:

  • To update and enhance the Operon DataBase (ODB) with new features for operon analysis and prediction.
  • To integrate high-throughput operon data and provide advanced visualization tools.

Main Methods:

  • Updated existing operon data and integrated new genome-wide transcriptional unit data for prokaryotes and eukaryotes.
  • Developed a novel operon prediction tool based on "reference operons" derived from clustering known operons.
  • Implemented new graphical interfaces for comparative analysis and visualization of operon structures across multiple genomes.

Main Results:

  • The updated ODB contains information on approximately 10,000 known operons in over 50 genomes and over 400,000 conserved operons from more than 1000 bacterial genomes.
  • The "reference operon" concept provides a more reliable method for predicting operons.
  • New graphical interfaces enable efficient comparative and visualization studies of operon organization.

Conclusions:

  • The 2011 update of ODB significantly expands its data content and introduces innovative tools for operon research.
  • ODB serves as a valuable resource for studying genome organization and gene regulation.