IMG 4 version of the integrated microbial genomes comparative analysis system

By Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Tanja Woyke, Marcel Huntemann and 7 more. Nucleic Acids Res., 2013

577 citations recorded by the source corpus.

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

Subfields: Ecology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/ab84eb6982c8e2f57385dc2618b3f112e2ff1130

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Citations in the corpus

Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, methodology): “Subsequently, COG annotations were included into the SEED database (4) and the possibility to compare newly sequenced genomes against COGs had been provided by the Integrated Microbial Genomes (IMG) system at the DOE’s Joint Genome Institute (5).”
Insights from 20 years of bacterial genome sequencing (2015, methodology): “We have analyzed the metadata of genomes publically available in the Integrated Microbial Genomes comparative analysis system (IMG) (Markowitz et al. 2014) and GOLD (Pagani et al.”
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies (2015, background): “64 Genes are labeled as coding DNA sequences (CDSs) and noncoding RNA genes, and certain annotation pipelines (eg, IMG/MER) also predict for regulatory elements such as clustered regularly interspaced short palindromic repeats (CRISPRs).”
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) (2015, methodology): “The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of bacterial and archaeal genomes included into the Integrated Microbial Genome (IMG) system [1].”
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification (2014, methodology): “In fact, an entry in GOLD and compliance with required metadata is a prerequisite to submit a project to the IMG systems for annotation.”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, methodology): “Other databases such as the DOE’s Joint Genome Institute Integrated Microbial Genomes & Microbiomes (JGI IMG/M) database (7), the PATRIC (Pathosystems Resource Integration Center) database (8) and Ensembl Bacteria (9) provide additional layers of information for the deposited genomes through integra”
IMG/M 4 version of the integrated metagenome comparative analysis system (2013, background): “Consequently, IMG/M consists of samples of microbial community (microbiome) aggregate genomes (metagenomes) integrated with IMG’s comprehensive set of genomes from all three domains of life: plasmids, viruses and genome fragments (1).”
PRISM 3: expanded prediction of natural product chemical structures from microbial genomes (2017, methodology): “For antimetabolites, bisindoles and phosphonatecontaining natural products, we conducted a homologybased search using the JGI-IMG browser (18) and manually generated structure predictions based on homology to known clusters.”
IMG/M: integrated genome and metagenome comparative data analysis system (2016, background): “The current version of the system (as of July 2016) contains a total of 47 516 (among them 40 894 public) archaeal, bacterial and eukaryotic genomes, which represents an over 300% increase since September 2013 (27).”