An experimental metagenome data management and analysis system
Open Access
- 15 July 2006
- journal article
- conference paper
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 22 (14) , e359-e367
- https://doi.org/10.1093/bioinformatics/btl217
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 . Contact:vmmarkowitz@lbl.govKeywords
This publication has 15 references indexed in Scilit:
- Genomic perspectives in microbial oceanographyNature, 2005
- Comparative Metagenomics of Microbial CommunitiesScience, 2005
- Cataloguing our current genome collectionMicrobiology, 2005
- Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial CommunitiesPLoS Computational Biology, 2005
- NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteinsNucleic Acids Research, 2004
- Environmental Genome Shotgun Sequencing of the Sargasso SeaScience, 2004
- Community structure and metabolism through reconstruction of microbial genomes from the environmentNature, 2004
- Missing genes in metabolic pathways: a comparative genomics approachCurrent Opinion in Chemical Biology, 2003
- Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripesScience, 2002
- An efficient algorithm for large-scale detection of protein familiesNucleic Acids Research, 2002