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Bioinformatics 2006 22(14):e359-e367; doi:10.1093/bioinformatics/btl217
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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An experimental metagenome data management and analysis system

Victor M. Markowitz 1,*, Natalia Ivanova 2, Krishna Palaniappan 1, Ernest Szeto 1, Frank Korzeniewski 1, Athanasios Lykidis 2, Iain Anderson 2, Konstantinos Mavrommatis 2, Victor Kunin 3, Hector Garcia Martin 3, Inna Dubchak 2, Phil Hugenholtz 3 and Nikos C. Kyrpides 2

1 Biological Data Management and Technology Center, Lawrence Berkeley National Lab USA
2 Genome Biology Program, Joint Genome Institute USA
3 Microbial Ecology Program, Joint Genome Institute USA

*To whom correspondence should be addressed.

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.

Contact: vmmarkowitz{at}lbl.gov


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