ArticleFrontiers in microbiology2014
Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes.
Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 83 citations in OpenAlex.
- Computational prediction of replication origins: a comparative review of methods, benchmarks, and trends from heuristics to deep learning.Briefings in bioinformatics · 2026Review
- OriV-Finder: a comprehensive web server for bacterial plasmid replication origin analysis.Nucleic acids research · 2025Article
- Description and Comparative Genomics ofLife (Basel, Switzerland) · 2025Article
- Atypical rhizobia trigger nodulation and pathogenesis on the same legume hosts.Nature communications · 2024Article
- Comparative analyses of persistence traits inFrontiers in microbiology · 2024Article
- Genomic and Phenotypic Characterization of Shiga Toxin-ProducingMicroorganisms · 2023Article
- ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion.Bioinformatics (Oxford, England) · 2023Article
- DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes.Nucleic acids research · 2023Article
- Article
- Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins.Genomics, proteomics & bioinformatics · 2022Article
- Comparative Genomics ofMicroorganisms · 2022Article
- Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny.Journal of microbiology (Seoul, Korea) · 2022Article
- Integrating LASSO Feature Selection and Soft Voting Classifier to Identify Origins of Replication Sites.Current genomics · 2022Article
- Complete Genome Sequence of the Type Strain Tepidimonas taiwanensis LMG 22826T, a Thermophilic Alkaline Protease and Polyhydroxyalkanoate Producer.Genome biology and evolution · 2021Article
- Genome structural variation inMicrobial genomics · 2021Article
- Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains.Genome biology and evolution · 2021Article
- Complete Closed Genome Sequence of the Extremely Heat-Resistant Strain Escherichia coli AW1.7.Microbiology resource announcements · 2021Article
- Computational prediction of species-specific yeast DNA replication origin via iterative feature representation.Briefings in bioinformatics · 2021Article
- Locus of Heat Resistance (LHR) in Meat-Borne Escherichia coli: Screening and Genetic Characterization.Applied and environmental microbiology · 2021Article
- A deep learning framework combined with word embedding to identify DNA replication origins.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA replication is one of the most basic processes in all three domains of cellular life. With the advent of the post-genomic era, the increasing number of complete archaeal genomes has created an opportunity for exploration of the molecular mechanisms for initiating cellular DNA replication by in vivo experiments as well as in silico analysis. However, the location of replication origins (oriCs) in many sequenced archaeal genomes remains unknown. We present a web-based tool Ori-Finder 2 to predict oriCs in the archaeal genomes automatically, based on the integrated method comprising the analysis of base composition asymmetry using the Z-curve method, the distribution of origin recognition boxes identified by FIMO tool, and the occurrence of genes frequently close to oriCs. The web server is also able to analyze the unannotated genome sequences by integrating with gene prediction pipelines and BLAST software for gene identification and function annotation. The result of the predicted oriCs is displayed as an HTML table, which offers an intuitive way to browse the result in graphical and tabular form. The software presented here is accurate for the genomes with single oriC, but it does not necessarily find all the origins of replication for the genomes with multiple oriCs. Ori-Finder 2 aims to become a useful platform for the identification and analysis of oriCs in the archaeal genomes, which would provide insight into the replication mechanisms in archaea. The web server is freely available at http://tubic.tju.edu.cn/Ori-Finder2/.
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