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OriV-Finder: a comprehensive web server for bacterial plasmid replication origin analysis.

Yujie Li1, Feng Gao1,2,3

  • 1Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.

Nucleic Acids Research
|April 29, 2025
PubMed
Summary
This summary is machine-generated.

OriV-Finder is a new web server that helps scientists find bacterial plasmid replication origins (oriVs). It uses replication initiation proteins (RIPs) and conserved features to accurately identify and prioritize potential oriVs.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Molecular Biology

Background:

  • Bacterial plasmids are crucial for horizontal gene transfer and adaptation.
  • Identifying vegetative replication origins (oriVs) is essential for understanding plasmid maintenance and replication.
  • Existing methods for oriV identification are often time-consuming and lack systematic analysis.

Purpose of the Study:

  • To develop a comprehensive and user-friendly web server for the rapid and systematic identification of bacterial plasmid replication origins (oriVs).
  • To provide a tool that accurately identifies potential oriVs based on replication initiation proteins (RIPs) and conserved features.

Main Methods:

  • Collected 470 replication initiation proteins (RIPs) from existing literature.
  • Identified 35 conserved domains associated with RIPs.
  • Developed a scoring system to assess the likelihood of intergenic sequences as potential oriVs, integrating RIP information and conserved features.

Main Results:

  • OriV-Finder accurately identifies homologous RIP genes.
  • The server assesses the likelihood of intergenic sequences being potential oriVs using a priority-based scoring system.
  • Integrated visualization modules for oriVs, RIPs, and genomes facilitate analysis and validation.

Conclusions:

  • OriV-Finder provides an efficient and accurate method for identifying bacterial plasmid replication origins.
  • The web server simplifies the analysis and validation of oriVs, aiding research in plasmid biology.
  • OriV-Finder is freely accessible, promoting wider use in the scientific community.