Work

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

Year: 2025

Type: article

Abstract: To rapidly identify and systematically analyse the vegetative replication origins (oriVs) of bacterial plasmids, we present OriV-Finder, a comprehensive web server for bacterial plasmid replication origin analysis. To fulfil this purpose, we collected 470 replication initiation proteins (RIPs) reported in the literature, identified 35 conserved domains associated with RIPs, and summarized conserved features of oriVs for various replication initiation mechanisms. Therefore, OriV-Finder could accurately identify the homologous genes of RIPs and then assess the likelihood of each intergenic sequence as a potential oriV based on the information of RIPs and conserved features. Consequently, the potential oriVs could be designated using a priority-based scoring system. As a user-friendly web server, OriV-Finder integrates visualization modules of oriVs, RIPs, and genomes, which facilitates the analysis and validation of oriVs. OriV-Finder is freely available to all users without any login requirement at https://tubic.org/OriV-Finder/.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkaf341

Authors: Yujie Li, Feng Gao

Institution: Tianjin University

Language: English

Topic: Bacterial Genetics and Biotechnology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,992

Funder: National Natural Science Foundation of China