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

By Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Manoj Pillay, Anna Ratner, Jinghua Huang, I. Pagani, Susannah Tringe and 8 more. 2013

274 citations recorded by the source corpus.

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 copewith 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).

Subfields: Ecology, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

Clustering huge protein sequence sets in linear time (2017, methodology): “59 billion protein sequence fragments predicted by Prodigal [19] in 2200 metagenomic and metatranscriptomic datasets [3, 20, 21] downloaded mainly 200”
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification (2014, methodology): “GOLD supports the IMG family of data management systems (9,13–15) as a gatekeeper of projects and metadata and requires that projects are annotated with at least minimal metadata.”
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles (2019, background): “…thaumarchaeal physiology that explain their ecological success and biogeochemical relevance, including an exceptionally high affinity for ammonia (Martens-Habbena et al. 2009), the production of the greenhouse gas nitrous oxide (Santoro et al. 2011), and other aspects of their metabolism related…”
IMG/M: integrated genome and metagenome comparative data analysis system (2016, background): “gov/mer/) of IMG it provides additional functions such as the listing of MyIMG gene annotations (30,31) and MyJob tracking of jobs submitted for computation on demand (33).”