The Integrated Microbial Genomes
IMG
system is a genome browsing and annotation platform developed by the U.S. Department of Energy (DOE)-

Joint Genome Institute The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), first located in Walnut Creek then Berkeley, California, was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and i ...

. IMG contains all the draft and complete microbial genomes sequenced by the DOE-JGI integrated with other publicly available genomes (including Archaea, Bacteria, Eukarya, Viruses and Plasmids). IMG provides users a set of tools for comparative analysis of microbial genomes along three dimensions: genes, genomes and functions. Users can select and transfer them in the comparative analysis carts based upon a variety of criteria. IMG also includes a genome annotation pipeline that integrates information from several tools, including

KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...

Pfam Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families. Uses ...

InterPro InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The contents of InterPro ...

, and the

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...

, among others. Users can also type or upload their own gene annotations (called MyIMG gene annotations) and the IMG system will allow them to generate

Genbank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...

EMBL The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...

format files containing these annotations. In successive releases IMG has expanded to include several domain-specific tools. The Integrated Microbial Genomes with Microbiome Samples''
(IMG/M)
system is an extension of the IMG system providing a comparative analysis context of assembled

metagenomic Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...

data with the publicly available isolate genomes. The Integrated Microbial Genomes- Expert Review''
(IMG/ER)
system provides support to individual scientists or group of scientists for functional annotation and curation of their microbial genomes of interest. Users can submit their annotated genomes (or request the IMG automated annotation pipeline to be applied first) into IMG-ER and proceed with manual curation and comparative analysis in the system, through secure (password protected) access. The IMG-HMP is focused on analysis of genomes related to the

Human Microbiome Project The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on i ...

(HMP) in the context of all publicly available genomes in IMG. The '
IMG-ABC
'' system is a system for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery. The '
IMG-VR
'' system (with the recent updated version IMG/VR v.2.0) is the largest publicly available database for viral genomes and metagenomes.

References

External links

*
IMG/M home page

MicrobesOnline

NCBI Microbial Genomes

TIGR Comprehensive Microbial Resource

The SEED
{{genomics-footer * Biological databases Pathogen genomics

See also

References

External links