proGenomes
proGenomes is a database providing consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes belonging to over 12,000 species. These can be interactively explored and downloaded, whereby subsets can be customized, e.g. taxonomic clades, representatives of each species or habitat-specific organisms.
Description
More detailed information about this field from each metasource.
proGenomes is a database providing consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes belonging to over 12,000 species. These can be interactively explored and downloaded, whereby subsets can be customized, e.g. taxonomic clades, representatives of each species or habitat-specific organisms.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
Webpage:
http://progenomes.embl.de/Webpage
More detailed information about this field from each metasource.
Licence:
Name: GPL-3.0Licence name
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Publications:
Publications
More detailed information about this field from each metasource.
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
PMID: 28053165
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
PMID: 31647096
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
Publications
More detailed information about this field from each metasource.
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
PMID: 28053165
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
PMID: 31647096
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
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proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
PubMed citations: 37.
37 articles citing: proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. PMID:35075131
Prokaryotic Genome Annotation. PMID:34718997
Positive Synergistic Effects of Quercetin and Rice Bran on Human Gut Microbiota Reduces Enterobacteriaceae Family Abundance and Elevates Propionate in a Bioreactor Model. PMID:34659185
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Dispersal strategies shape persistence and evolution of human gut bacteria. PMID:34111423
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PMID:33868800
Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy. PMID:33859339
Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota. PMID:33808469
Origin Sample Prediction and Spatial Modeling of Antimicrobial Resistance in Metagenomic Sequencing Data. PMID:33763122
The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis. PMID:33681304
Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PMID:33561170
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. PMID:33436509
Rewiring the specificity of extracytoplasmic function sigma factors. PMID:33318184
Prevalence of phase variable epigenetic invertons among host-associated bacteria. PMID:33119758
Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. PMID:33072721
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. PMID:32047279
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines. PMID:32025702
Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly. PMID:32019832
Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. PMID:32019803
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
CAMITAX: Taxon labels for microbial genomes. PMID:31909794
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. PMID:31647096
Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre. PMID:31632377
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
GMrepo: a database of curated and consistently annotated human gut metagenomes. PMID:31504765
The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity. PMID:31501539
Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship. PMID:30949677
Microbial abundance, activity and population genomic profiling with mOTUs2. PMID:30833550
Co-culture and biogeography of Prochlorococcus and SAR11. PMID:30742057
Antibiotics-induced monodominance of a novel gut bacterial order. PMID:30658995
Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. PMID:30630933
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. PMID:30381904
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. PMID:29771380
Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment. PMID:29235508
MVP: a microbe-phage interaction database. PMID:29177508
metaSNV: A tool for metagenomic strain level analysis. PMID:28753663 -
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
PubMed citations: 16.
16 articles citing: proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. PMID:35264791
Genome-wide identification and expression analysis of HAK/KUP/KT potassium transporter provides insights into genes involved in responding to potassium deficiency and salt stress in pepper (Capsicum annuum L.). PMID:35251880
Contamination detection in genomic data: more is not enough. PMID:35189924
Towards the biogeography of prokaryotic genes. PMID:34912116
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes. PMID:34791031
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. PMID:34665009
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria. PMID:34546073
'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life. PMID:34357062
Amine oxidase, copper containing 3 exerts anti‑mesenchymal transformation and enhances CD4+ T‑cell recruitment to prolong survival in lung cancer. PMID:34318901
Identification of antigenic domains and peptides from VP15 of white spot syndrome virus and their antiviral effects in Marsupenaeus japonicus. PMID:34140570
GUNC: detection of chimerism and contamination in prokaryotic genomes. PMID:34120611
Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes. PMID:33815284
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. PMID:33372654
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. PMID:32047279
Tags:
Tags
More detailed information about this field from each metasource.
metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
data submission, annotation and curation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
taxonomy
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
Tags
More detailed information about this field from each metasource.
metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
data submission, annotation and curation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
taxonomy
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
metagenomics genomics data submission, annotation and curation taxonomy
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