Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins

The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated at genomic loci referred to as replication origins ( oriC s). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriC s in 2008 called Ori-Finder, which contributes to clarify the characteristics of bacterial oriC s. The oriC s of hundreds of sequenced bacterial genomes have been annotated in their genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of oriC s. This has facilitated large-scale data mining of functional elements in oriC s and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of oriC s are integrated into the updated framework, which has also been redesigned to predict oriC s in draft genomes. The interactive visualization module displays more genomic information related to oriC s and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses. The redesigned interface provides additional customization options for oriC prediction. Ori-Finder 2022 is freely available at http://tubic.tju.edu.cn/Ori-Finder2022 and https://tubic.org/Ori-Finder2022 .