IMG/M 4 version of the integrated metagenome comparative analysis system

Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah; Huntemann, Marcel; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N.; Kyrpides, Nikos C.

doi:10.1093/nar/gkt919

Title: IMG/M 4 version of the integrated metagenome comparative analysis system

Journal Article · Wed Oct 16 00:00:00 EDT 2013 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkt919· OSTI ID:1625530

Markowitz, Victor M. ^[1]; Chen, I-Min A. ^[1]; Chu, Ken ^[1]; Szeto, Ernest ^[1]; Palaniappan, Krishna ^[1]; Pillay, Manoj ^[1]; Ratner, Anna ^[1]; Huang, Jinghua ^[1]; Pagani, Ioanna ^[2]; Tringe, Susannah ^[2]; Huntemann, Marcel ^[2]; Billis, Konstantinos ^[2]; Varghese, Neha ^[2]; Tennessen, Kristin ^[2]; Mavromatis, Konstantinos ^[2]; Pati, Amrita ^[2]; Ivanova, Natalia N. ^[2]; Kyrpides, Nikos C. ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division. Biological Data Management and Technology Center
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program

IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M’s data content and analytical tools have expanded continuously since its first version was released in 2007. Since the last report published in the 2012 NAR Database Issue, IMG/M’s database architecture, annotation and data integration pipelines and analysis tools have been extended to cope with the rapid growth in the number and size of metagenome data sets handled by the system. IMG/M data marts provide support for the analysis of publicly available genomes, expert review of metagenome annotations (IMG/M ER: http://img.jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/ imgm_hmp).

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625530

Journal Information:: Nucleic Acids Research, Vol. 42, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers Lünse, Christina E.; Weinberg, Zasha; Breaker, Ronald R. Taylor & Francis https://doi.org/10.6084/m9.figshare.4239683.v1	text	January 2016
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Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation González, Carolina; Lazcano, Marcelo; Valdés, Jorge Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.02035	journal	December 2016
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Genomic Characteristics of Desulfonema ishimotonii Tokyo 01T Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria Watanabe, Miho; Kojima, Hisaya; Umezawa, Kazuhiro Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00227	journal	February 2019
The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response Erill, Ivan; Campoy, Susana; Kılıç, Sefa Frontiers in Molecular Biosciences, Vol. 3 https://doi.org/10.3389/fmolb.2016.00033	journal	July 2016
A Bioinformatics Guide to Plant Microbiome Analysis Lucaciu, Rares; Pelikan, Claus; Gerner, Samuel M. Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01313	journal	October 2019
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