title: An experimental metagenome data management and analysis system.
abstract: The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m.
authors.affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Lab, USA. vmmarkowitz@lbl.gov
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Krishna
authors.initials: K
authors.lastname: Palaniappan
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.forename: Frank
authors.initials: F
authors.lastname: Korzeniewski
authors.forename: Athanasios
authors.initials: A
authors.lastname: Lykidis
authors.forename: Iain
authors.initials: I
authors.lastname: Anderson
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavrommatis
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.forename: Hector
authors.initials: H
authors.lastname: Garcia Martin
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.forename: Phil
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
mesh_terms: D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000502:physiology*; D003628:Database Management Systems; D030541:Databases, Genetic; D016680:Genome, Bacterial / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D020543:Proteome