A5050011808- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- Gut microbiota and health
- Advanced Database Systems and Queries
- Polar Research and Ecology
- Environmental DNA in Biodiversity Studies
- Plant nutrient uptake and metabolism
- Marine and coastal ecosystems
- Microbial Natural Products and Biosynthesis
- Protist diversity and phylogeny
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- Plant Virus Research Studies
- Plant Pathogenic Bacteria Studies
- Semantic Web and Ontologies
- Climate change and permafrost
- Mycobacterium research and diagnosis
- Biofuel production and bioconversion
- Coastal wetland ecosystem dynamics
- Biocrusts and Microbial Ecology
- Machine Learning in Bioinformatics
- Research Data Management Practices
- Geological Studies and Exploration
Joint Genome Institute
2013-2025
Lawrence Berkeley National Laboratory
2015-2025
United States Department of Energy
1993-2022
National Tsing Hua University
2019
Bioscience (China)
2016
National Energy Research Scientific Computing Center
2015
Chung Shan Medical University
2013
Los Alamos National Laboratory
2013
National Yang Ming Chiao Tung University
2013
Taipei Veterans General Hospital
2013
The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables search page. As September 2009, contains information more than 5800 sequencing which 1100 have been completed sequence data deposited public repository. continues to expand, moving toward the goal providing most repository metadata related...
A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and eventually included into various public genome data resources. The quality the annotations depends largely on original dataset providers, with erroneous or incomplete often carried over resources difficult to correct.We have developed an Expert Review (ER) version Integrated Microbial Genomes (IMG) system, goal supporting systematic efficient revision annotations. IMG ER provides tools for review...
The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source include those generated by the DOE's Joint Genome Institute (JGI), submitted external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed...
Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled...
The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well plasmids, viruses and genome fragments. IMG provides tools for analyzing reviewing the structural functional annotations in a comparative context. IMG's content analytical capabilities have increased continuously since its first version released 2005. Since last report published 2012 NAR Database Issue, annotation integration pipelines evolved while new been added recording single...
The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic viral genomes from cultured organisms, (ii) single cell (SCG) metagenomes (GFM) uncultured archaea, bacteria viruses (iii) environmental, host associated engineered microbiome samples. Sequence are generated by DOE's Joint Genome Institute (JGI), submitted individual scientists, or collected public archives....
Abstract The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) contains annotated isolate genome and metagenome datasets sequenced at the DOE’s Joint Genome Institute (JGI), submitted by external users, or imported from public sources such as NCBI. IMG v 6.0 includes advanced search functions a new tool for statistical analysis of mixed sets genomes bins. web user interface also has Help page with additional documentation webinar tutorials to help...
Abstract The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets provided via IMG submission site. Dataset for first requires project associated metadata description in GOLD. data processing consists feature prediction including identification protein-coding genes, non-coding RNAs regulatory RNA...
Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections their cellular hosts, viruses can reshape microbial community structure drive global nutrient cycling. Over the past decade, viral sequences identified from genomes metagenomes have provided an unprecedented view genome diversity in nature. Since 2016, IMG/VR database has access to largest collection obtained (meta)genomes. Here, we present third version IMG/VR, composed 18 373 cultivated...
IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context a comprehensive set reference from all three domains life, as well plasmids, viruses and genome fragments. IMG/M’s data content analytical tools have expanded continuously since its first version was released 2007. Since last report published 2012 NAR Database Issue, database architecture, annotation integration pipelines been extended to copewith...
Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration the global virosphere, progressively revealing extensive genomic diversity viruses on Earth and highlighting myriad ways by which impact biological processes. IMG/VR provides access to largest collection viral sequences obtained from (meta)genomes, along with functional annotation rich metadata. A web interface users efficiently browse search based genome features and/or...
The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users perform comparative analysis isolate and single cell genomes, metagenomes, metatranscriptomes. In addition datasets produced by JGI, IMG v.7 also includes imported from public sources such as NCBI Genbank, SRA, DOE National Microbiome Data Collaborative (NMDC), or submitted external users. past couple...
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains up-to-date catalog of genome and metagenome projects in the context a comprehensive list associated metadata. Information GOLD organized into four levels: Study, Biosample/Organism, Sequencing Project Analysis Project. Currently hosts information on 33 415 Studies, 49 826 Biosamples, 313 324 Organisms, 215 881 Projects 174 454 with total 541 metadata fields, 80 are based controlled...
Abstract The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world. current version database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) Analysis (283 481). These four levels contain 600 fields, which 76 controlled vocabulary (CV) tables containing 3873 terms....
Abstract The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one flagship genomic metadata repositories world. ever-increasing number projects and are freely available user community world-wide. GOLD’s is consumed by scientists remains an important source for large-scale comparative genomics analysis initiatives. Encouraged this active engagement growth, GOLD has continued add new...
The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available in comprehensive context. IMG contains both draft and complete with other from all three domains life, together large number plasmids viruses. provides tools viewers analyzing reviewing the annotations genes Since its first release 2005, IMG's data content analytical capabilities have been constantly expanded through regular releases. Several companion systems set up...
The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Genome (IMG) system. MAP is applied on nucleotide sequence datasets included in IMG-ER (Expert Review) version IMG via ER submission site. Users can submit consisting one or more contigs a multi-fasta file. includes protein coding and RNA genes, as well repeats assignment product names to these genes.
The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. Since last report published in 2016, NAR Database Issue, has tripled size currently contains genomes of 8389 cultivated reference viruses, 12 498 previously curated prophages derived from microbial isolates, 735 112 genomic fragments computationally predicted assembled shotgun metagenomes. Nearly 60%...
The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system comparative analysis. pipeline runs on nucleotide provided via IMG submission site. Users must first define their analysis projects in GOLD then submit associated sequence datasets consisting of scaffolds/contigs optional coverage information and/or unassembled reads fasta fastq file...
Microbial secondary metabolism is a reservoir of bioactive compounds immense biotechnological and biomedical potential. The biosynthetic machinery responsible for the production these metabolites (SMs) (also called natural products) often encoded by collocated groups genes gene clusters (BGCs). High-throughput genome sequencing both isolates metagenomic samples combined with development specialized computational workflows enabling systematic identification BGCs discovery novel SMs. In order...
The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs preprocessing, error correction, assembly, structural and functional annotation, binning.
Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded clusters co-located genes called biosynthetic gene (BCs). In order advance the exploration microbial secondary metabolism, we developed largest publically available database experimentally verified...
The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae renowned producers of secondary metabolites commercial interest, yet only a small part its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context phylum-wide analysis 6,700 including public isolates metagenome-assembled (MAGs). We estimate that 30%–50% projected phylogenetic possesses genomic representation...
Abstract Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological evolutionary processes within microbial communities, hold substantial importance human health biotechnology. To support plasmid research provide scientists with data an unprecedented diversity sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 sequences derived from genomes, metagenomes metatranscriptomes. is first...