Journal Article Ppublish
PubMed: 40297992 DOI: 10.1093/nar/gkaf341
OriV-Finder: a comprehensive web server for bacterial plasmid replication origin analysis.
Nucleic Acids Res 53(W1):W451-W456
Authors: Yujie Li, Feng Gao
Affiliations
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China. State Key Laboratory of Synthetic Biology, Tianjin University, Tianjin 300072, China. Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin300072, China.
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/.
MeSH
Nucleic Acids, Replication Origin, Plasmids