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

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) 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

[1]  Lior Pachter,et al.  Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities , 2005, PLoS Comput. Biol..

[2]  Bernd Hamann,et al.  SNP-VISTA: An interactive SNP visualization tool , 2005, BMC Bioinformatics.

[3]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[4]  I-Min A. Chen,et al.  The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions , 2007, Nucleic Acids Res..

[5]  A. Salamov,et al.  Use of simulated data sets to evaluate the fidelity of metagenomic processing methods , 2007, Nature Methods.

[6]  Inna Dubchak,et al.  The integrated microbial genomes (IMG) system , 2005, Nucleic Acids Res..

[7]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[8]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide , 2005, Nucleic Acids Res..

[9]  Natalia N. Ivanova,et al.  Symbiosis insights through metagenomic analysis of a microbial consortium. , 2006, Nature Reviews Microbiology.

[10]  Natalia Ivanova,et al.  Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities , 2006, Nature Biotechnology.

[11]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[12]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[13]  Inna Dubchak,et al.  An experimental metagenome data management and analysis system , 2006, ISMB.

[14]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[15]  Mihai Pop,et al.  Microbiome Metagenomic Analysis of the Human Distal Gut , 2009 .

[16]  Renzo Kottmann,et al.  eGenomics: Cataloguing Our Complete Genome Collection III , 2007, Comparative and Functional Genomics.

[17]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[18]  Benjamin A. Shoemaker,et al.  CDD: a database of conserved domain alignments with links to domain three-dimensional structure , 2002, Nucleic Acids Res..