ArticleGenomics, proteomics & bioinformatics2022
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins.
Article in Genomics, proteomics & bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed.
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- Glucose-dependent acidification strategy by nectar-dwelling bacteria mediates pollen tube burst.Nature communications · 2026Article
- Computational prediction of replication origins: a comparative review of methods, benchmarks, and trends from heuristics to deep learning.Briefings in bioinformatics · 2026Review
- SSB-mediated enhancement of argonaute activity triggers SOS filamentation in bacteria.Nucleic acids research · 2026Article
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- Genome report: chromosome-scale genome assembly of the olive fly Bactrocera oleae (Diptera: Tephritidae).G3 (Bethesda, Md.) · 2026Article
- Lineage-restricted genomic islands drive rhizosphere niche specialization inISME communications · 2026Article
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- Genome-Based Reclassification of [Microorganisms · 2025Article
- Elevated rates and biased spectra of mutations in anaerobically cultured lactic acid bacteria.mBio · 2025Article
- Biotechnological potential and genomic analysis of the Leuconostoc mesenteroides F17 and F18 strains isolated from camel milk.BMC microbiology · 2025Article
- Unlocking the genomic repertoire of a cultivated megaphage.Npj viruses · 2025Article
- Creating a consensus genome assembly ofNAR genomics and bioinformatics · 2025Article
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3 authors.
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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 is helpful to clarify the characteristics of bacterial oriCs. The oriCs of hundreds of sequenced bacterial genomes have been annotated in the 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-Finder/ and https://tubic.org/Ori-Finder/.
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