DNA replication initiates on defined genome sites, termed replication origins, in all three domains of life. The research on replication origins is important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The availability of increasing complete bacterial genomes has created challenges and opportunities for identification of their oriCs in silico simultaneously. Based on the Z-curve theory, with the means of comparative genomics, we have developed the web-based system Ori-Finder for finding replication origins (oriCs) in bacterial genomes with high accuracy and reliability, which have been applied to annotate oriCs in newly sequenced bacterial genomes including those published in Nature (Graf et al., Nature, 2021) and Nature Microbiology (Needham et al., Nature Microbiology, 2022). Ori-Finder has also been referred as a software tool to identify replichores recently (Wannier et al., Nature Reviews Methods Primers, 2021). Currently, the predicted replication origins in dozens of bacteria have been confirmed by experiments, and the predictions have also been supported by the studies published in Science (Korem et al., Science, 2015) and Nature (Richardson et al., Nature, 2016).

Therefore, in order to integrate the latest research results about bacterial replication origins and improve user experience, we present Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. The following is the main workflow of Ori-Finder 2022. Please refer to our article (in press) for details.

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Citation
  • Dong, M-J#, Luo, H#, Gao, F*: Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins, Genomics, Proteomics & Bioinformatics, in press.

We welcome any feedback or corrections regarding the web server, and if you have any questions about Ori-Finder, please don't hesitate to contact us ( fgao@tju.edu.cn). We will reply to you as soon as possible.