ArticleNucleic acids research2017
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- The heterogeneous selection landscape of genome evolution in prokaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The heterogeneous selection landscape of genome evolution in prokaryotes.Research square · 2025Article
- Glyphosate and phosphate treatments in soil differentially affect crop microbiomes depending on species, tissue and growth stage.Scientific reports · 2025Article
- Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.bioRxiv : the preprint server for biology · 2025Article
- The Effect of the Presence and Absence of DNA Repair Genes on the Rate and Pattern of Mutation in Bacteria.Genome biology and evolution · 2024Article
- No Evidence that Selection on Synonymous Codon Usage Affects Patterns of Protein Evolution in Bacteria.Genome biology and evolution · 2024Article
- Does Glyphosate Affect the Human Microbiota?Life (Basel, Switzerland) · 2022Article
- Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century.Trends in microbiology · 2021Review
- Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events.International journal of molecular sciences · 2021Article
- Article
- Are Nonsynonymous Transversions Generally More Deleterious than Nonsynonymous Transitions?Molecular biology and evolution · 2021Article
- Endogenous CRISPR-Cas Systems in Group IFrontiers in microbiology · 2021Article
- CRISPR Arrays Away fromThe CRISPR journal · 2020Article
- Impact of C-terminal amino acid composition on protein expression in bacteria.Molecular systems biology · 2020Article
- Crossing fitness valleys via double substitutions within codons.BMC biology · 2019Article
- Amino acid exchangeabilities vary across the tree of life.Science advances · 2019Article
- Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence.Nature communications · 2019Article
- Linking high GC content to the repair of double strand breaks in prokaryotic genomes.PLoS genetics · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of 'index' orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html.
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