ArticleNucleic acids research2020
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.JHEP reports : innovation in hepatology · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
- proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.Nucleic acids research · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- Alterations of the Upper Respiratory Microbiome Among Children Living With HIV Infection in Botswana.The Journal of infectious diseases · 2025Article
- Swarm-seq Reveals Functional Divergence in CsrA Homologs Across Bacteria.bioRxiv : the preprint server for biology · 2025Article
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- Genomic analysis of three medieval parchments from German monasteries.Scientific reports · 2025Article
- Genomic insights intoFrontiers in microbiology · 2025Article
- A catalog of small proteins from the global microbiome.Nature communications · 2024Article
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- Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.Microbial ecology · 2024Article
- Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries.Nature communications · 2024Article
- Airway microbiome signature accurately discriminatesiScience · 2024Article
- Review
- Putative genome contamination has minimal impact on the GTDB taxonomy.Microbial genomics · 2024Article
- Toxicological Characteristics of Bacterial Nanocellulose in an In Vivo Experiment-Part 1: The Systemic Effects.Nanomaterials (Basel, Switzerland) · 2024Article
- Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung.Nature communications · 2024Article
- Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.Scientific reports · 2024Article
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Authors and funding
14 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Microbiology depends on the availability of annotated microbial genomes for many applications. Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved individually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database. The database is available at http://progenomes.embl.de/.
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