ArticleNucleic acids research2019
DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed, 96 citations in OpenAlex.
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- Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis.Briefings in bioinformatics · 2023Article
- Article
- The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India.Archives of microbiology · 2023Article
- Whole-Genome Sequence of Salmonella enterica Serovar Bispebjerg from Turkey Reveals Its Pathogenic Potential.Microbiology resource announcements · 2023Article
- DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes.Nucleic acids research · 2023Article
- Replication-associated inversions are the dominant form of bacterial chromosome structural variation.Life science alliance · 2023Article
- Obligate autotrophy at the thermodynamic limit of life in a new acetogenic bacterium.Frontiers in microbiology · 2023Article
- Characterization of a novel theta-type replicon of indigenous plasmid pTE15 from Lactobacillus reuteri N16.BMC microbiology · 2022Article
- The Caulobacter crescentus DciA promotes chromosome replication through topological loading of the DnaB replicative helicase at replication forks.Nucleic acids research · 2022Article
- Recombineering in Non-Model Bacteria.Current protocols · 2022Article
- Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins.Genomics, proteomics & bioinformatics · 2022Article
- Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria.Microbial genomics · 2022Article
- Genomic structural plasticity of rodent-associated Bartonella in nature.Molecular ecology · 2022Article
- Reply to: Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes.Nature communications · 2022Article
- A Highly Unstable and Elusive Plasmid That Encodes the Type III Secretion System Is Necessary for Full Virulence in the Marine Fish PathogenInternational journal of molecular sciences · 2022Article
- Characterisation of the symbionts in the Mediterranean fruit fly gut.Microbial genomics · 2022Article
- SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids.Scientific data · 2022Article
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.Genome research · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007. DoriC 5.0, an updated database of oriC regions in both bacterial and archaeal genomes, was published in the 2013 Nucleic Acids Research database issue. Now, the latest release DoriC 10, a large-scale update of replication origins in prokaryotic genomes including chromosomes and plasmids, has been presented with a completely redesigned user interface, which is freely available at http://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/. In the current release, the database of DoriC has made significant improvements compared with version 5.0 as follows: (i) inclusion of oriCs on more bacterial chromosomes increased from 1633 to 7580; (ii) inclusion of oriCs on more archaeal chromosomes increased from 86 to 226; (iii) inclusion of 1209 plasmid replication origins retrieved from NCBI annotations or predicted by in silico analysis; (iv) inclusion of more replication origin elements on bacterial chromosomes including DnaA-trio motifs. Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication origin predictions.
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