IMG/M: A data management and analysis system for metagenomes

Journal Article · Wed Aug 01 00:00:00 EDT 2007 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkm869· OSTI ID:932562

Markowitz, Victor M; Ivanova, Natalia N; Szeto, Ernest; Palaniappan, Krishna; Chu, Ken; Dalevi, Daniel; Chen, I-Min A; Grechkin, Yuri; Dubchak, Inna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Hug enholtz, Phil; Kyrpides, Nikos C

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m. Studies of the collective genomes (also known as metagenomes) of environmental microbial communities (also known as microbiomes) are expected to lead to advances in environmental cleanup, agriculture, industrial processes, alternative energy production, and human health (1). Metagenomes of specific microbiome samples are sequenced by organizations worldwide, such as the Department of Energy's (DOE) Joint Genome Institute (JGI), the Venter Institute and the Washington University in St. Louis using different sequencing strategies, technology platforms, and annotation procedures. According to the Genomes OnLine Database, about 28 metagenome studies have been published to date, with over 60 other projects ongoing and more in the process of being launched (2). The Department of Energy's (DOE) Joint Genome Institute (JGI) is one of the major contributors of metagenome sequence data, currently sequencing more than 50% of the reported metagenome projects worldwide. Due to the higher complexity, inherent incompleteness, and lower quality of metagenome sequence data, traditional assembly, gene prediction, and annotation methods do not perform on these datasets as well as they do on isolate microbial genome sequences (3, 4). In spite of these limitations, metagenome data are amenable to a variety of analyses, as illustrated by several recent studies (5-10). Metagenome data analysis is usually set up in the context of reference isolate genomes and considers the questions of composition and functional or metabolic potential of individual microbiomes, as well as differences between microbiome samples. Such analysis relies on efficient management of genome and metagenome data collected from multiple sources, while taking into account the iterative nature of sequence data generation and processing. IMG/M aims at providing support for comparative metagenome analysis in the integrated context of microbial genome and metagenome data generated with diverse sequencing technology platforms and data processing methods.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Director. Office of Science. Biological andEnvironmental Research
• DOE Contract Number: DE-AC02-05CH11231
• OSTI ID: 932562
• Report Number(s): LBNL-63514; NARHAD; R&D Project: 626869; BnR: KP1103010; TRN: US200813%%117
• Journal Information: Nucleic Acids Research, Vol. 36; Related Information: Journal Publication Date: 2008; ISSN 0305-1048
• Country of Publication: United States
• Language: English

Related Subjects

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AGRICULTURE
COMMUNITIES
DATA ANALYSIS
DATA PROCESSING
FORECASTING
FUNCTIONALS
GENES
MANAGEMENT
PROCESSING
PRODUCTION