An experimental metagenome data management and analysis system

Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system. In: Philip E. Bourne and Soren Brunak, ISMB 2006 Conference proceedings. 14th Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, (e359-e367). 6-10 August 2006. doi:10.1093/bioinformatics/btl217

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Author Markowitz, Victor M.
Ivanova, Natalia
Palaniappan, Krishna
Szeto, Ernest
Korzeniewski, Frank
Lykidis, Athanasios
Anderson, Iain
Mavrommatis, Konstantinos
Kunin, Victor
Martin, Hector Garcia
Dubchak, Inna
Hugenholtz, Phil
Kyrpides, Nikos C.
Title of paper An experimental metagenome data management and analysis system
Conference name 14th Conference on Intelligent Systems for Molecular Biology (ISMB 2006)
Conference location Fortaleza, Brazil
Conference dates 6-10 August 2006
Proceedings title ISMB 2006 Conference proceedings   Check publisher's open access policy
Journal name Bioinformatics   Check publisher's open access policy
Place of Publication Oxford, U.K.
Publisher Oxford University Press
Publication Year 2006
Sub-type Fully published paper
DOI 10.1093/bioinformatics/btl217
ISSN 1367-4803
1367-4811
Editor Philip E. Bourne
Soren Brunak
Volume 22
Issue 14
Start page e359
End page e367
Total pages 9
Language eng
Abstract/Summary 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.
Keyword Protein families
Microbial communities
Sequence database
Genomes
Sea
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes This volume contains the papers accepted for presentation at the 2006 Intelligent Systems for Molecular Biology conference (ISMB 2006; www.iscb.org/ismb2006) held in Fortaleza, Brazil from August 6-10, 2006.

Document type: Conference Paper
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School of Chemistry and Molecular Biosciences
 
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