DOOR 2.0: presenting operons and their functions through dynamic and integrated views.

Area of Science:

• Genomics
• Bioinformatics
• Systems Biology

Background:

• Operons are fundamental genetic units in prokaryotes, crucial for gene regulation.
• Previous versions of the DOOR database provided valuable operon information but required expansion.
• Advances in sequencing and computational methods enable more comprehensive operon analysis.

Purpose of the Study:

• To introduce DOOR 2.0, a significantly enhanced and expanded operon database.
• To integrate diverse functional and regulatory data for prokaryotic operons.
• To provide advanced tools for operon prediction and data visualization.

Main Methods:

• Curated and computationally predicted operons from 2072 complete prokaryotic genomes.
• Integration of RNA-sequencing data for transcription unit identification and gene expression estimation.
• Development of a web service for de novo operon prediction.
• Implementation of a genome browser and a search engine for data exploration.

Main Results:

• DOOR 2.0 encompasses operons for 2072 prokaryotes, a threefold increase from the previous version.
• Includes over 250,000 transcription units with experimental or RNA-seq-based predictions.
• Provides integrated operon-centric data: regulatory sites, gene expression, and cross-genome conservation.
• Offers a high-performance prediction service and an intuitive visualization tool.

Conclusions:

• DOOR 2.0 represents a major advancement in prokaryotic operon annotation and analysis.
• The database facilitates dynamic functional and regulatory studies of operons.
• It serves as a comprehensive resource for researchers investigating prokaryotic gene organization and regulation.