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PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters.

Wei Su1, Meng-Lu Liu1, Yu-He Yang1

  • 1Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.

Journal of Molecular Biology
|February 4, 2021
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Summary
This summary is machine-generated.

Researchers have created the Prokaryotic Promoter Database (PPD), a new resource cataloging experimentally validated prokaryotic promoters. This database aids in exploring gene regulation across diverse prokaryotic species.

Keywords:
dRNA-seqgeneprokaryotepromotertranscription start site

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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.