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.
Ori-Finder 2022 can consequently handle complete or draft bacterial genomes in FASTA or GBK format.
Updated prediction framework
The updated prediction framework of Ori-Finder 2022 adopts a new scoring criterion to quantitatively reflect these oriC
Ori-Finder 2022 scores the characteristics of base composition according to the distance to the minimum of the GC disparity.
Bacterial oriCs are usually adjacent to a dnaA gene, which can sever as an indicator for oriCs, but such genes are often different among bacterial species.
Ori-Finder 2022 scores the characteristics of indicator genes, which can be adjusted based on the lineage and chromosome type entered by the user.
Ori-Finder 2022 scores DnaA boxes according to their numbers and mismatches.
In addition, Ori-Finder 2022 identifies other functional elements of oriC, such as the Dam methylation site (GATC), the binding site for the response regulator CtrA, and DnaA-trio, to screen prediction results.
Updated visualization and analysis module
Global or local information of the genome can be grasped at a glance from the interactive Z-curve graph that displays the four disparity curves and the distribution of DnaA boxes, indicator genes, potential oriCs, and replication terminus.
The characteristic visualization of oriC sequence displays the distribution of its functional elements,
such as DnaA box, DnaA-trio, ATP-DnaA box, GATC motif, and binding sites of CtrA, Fis, and IHF found in the predicted oriCs.
The peaks of the line graph calculated by SIST may correspond to the AT-rich sequence that might serve as a DNA unwinding element (DUE).
The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses.
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 ( email@example.com). We will reply to you as soon as