PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Promoters are crucial for transcription regulation in all domains of life.
• Existing databases like EPD focus on eukaryotic RNA polymerase II promoters.
• Prokaryotic promoter information is fragmented across literature, hindering research.

Purpose of the Study:

• To establish a centralized, comprehensive database of experimentally validated prokaryotic promoters.
• To facilitate the study of prokaryotic gene transcription and regulation.

Main Methods:

• Manual extraction of promoter data from published scientific articles.
• Curation of promoter information across 63 prokaryotic species.
• Development of a user-friendly web interface for data access and analysis.

Main Results:

• The Prokaryotic Promoter Database (PPD) now contains 129,148 validated prokaryotic promoters.
• The database covers 63 diverse prokaryotic species.
• A web interface allows browsing, searching, BLAST analysis, visualization, submission, and data download.

Conclusions:

• The PPD offers a valuable and comprehensive resource for prokaryotic gene transcription research.
• This database simplifies access to scattered prokaryotic promoter information.
• The PPD is freely available to the scientific community.