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Nucleic Acids Res. 2017 Jan 4;45(D1):D507-D516. doi: 10.1093/nar/gkw929. Epub 2016 Oct 13.

IMG/M: integrated genome and metagenome comparative data analysis system.

Author information

1
Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA IMAChen@lbl.gov.
2
Biosciences Computing Group, Computational Science Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
3
Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
4
Microbial Genome and Metagenome Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA nckyrpides@lbl.gov.

Abstract

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 and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

PMID:
27738135
PMCID:
PMC5210632
DOI:
10.1093/nar/gkw929
[Indexed for MEDLINE]
Free PMC Article

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