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

Abstract

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 (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriCs in 2008 called Ori-Finder, which contributes to clarify the characteristics of bacterial oriCs. The oriCs 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 oriCs. This has facilitated large-scale data mining of functional elements in oriCs 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 oriCs are integrated into the updated framework, which has also been redesigned to predict oriCs in draft genomes. The interactive visualization module displays more genomic information related to oriCs 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.

DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes

“…Complete and draft genomes together with their available annotation files were downloaded from the NCBI RefSeq database ( https://www.ncbi.nlm.nih.gov/refseq/ ) on 9 April 2022 ( 21 , 22 ). First, the oriC s in bacterial genomes were predicted using Ori-Finder 2022 ( https://tubic.org/Ori-Finder2022/ ) ( 23 ), an updated version of Ori-Finder, which adopts a new scoring system to consider the currently available oriC characteristics comprehensively and shows better prediction performance compared with the original version. Then, the predicted oriC s were added to the DoriC database after manual curation.…”

Complete Genome Sequence of Deinococcus aquaticus Type Strain PB314, a Non-Extremophile Representative of the Genus Deinococcus

“…Assembly quality was determined with QUAST v5.2.0+galaxy0 ( 12 ) and the Bacterial and Viral Bioinformatics Resource Center’s BV-BRC v3.27.7 ( https://www.bv-brc.org ) ( 13 ). The hybrid assembly showed high quality and contiguity with a total aligned length of 3,874,397 bp and an N 50 of 3.13 Mbp, consisting of 5 replicons ( Table 1 ), confirmed by Ori-Finder v2022 ( 14 ). Gene content was assessed by BUSCO v5.3.2+galaxy0 ( 15 ) and showed 90.3% completeness (single copy, 90.3%; duplicate, 0.0%; fragmented, 4.8%; missing, 4.9%; n = 124).…”

Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

“…While CheckV is primarily designed to estimate completeness of candidate viral genomes, we found that sequences with either low, medium or high scores were typically identified as viral by other tools as well (see Figure 3 in main text). Plasmid sequences were predicted using PlasFlow (v1.1.0)w [45] and PlasClass (v0.1) [46] and, if relevant, the origin of replication with OriFinder 2022 [67]. ICEs were identified with ICEfinder [47].…”