2009
DOI: 10.1093/nar/gkp887
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Abstract: The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005,… Show more

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Cited by 233 publications
(234 citation statements)
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“…An initial data set of all annotated Crp/Fnr genes in all currently available SRB genomes was compiled by extracting the genes from the Joint Genome Institute Integrated Microbial Genomes database (33). Additional reference sequences were also extracted based on homology to SRB sequences to obtain a representative data set of the major Crp/Fnr subfamilies.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…An initial data set of all annotated Crp/Fnr genes in all currently available SRB genomes was compiled by extracting the genes from the Joint Genome Institute Integrated Microbial Genomes database (33). Additional reference sequences were also extracted based on homology to SRB sequences to obtain a representative data set of the major Crp/Fnr subfamilies.…”
Section: Methodsmentioning
confidence: 99%
“…T ranscription factors, promoter sequences, and regulatory circuit architecture are often referred as "the regulatory genome" (27,33), and transcription factors are central to the function of regulatory networks (5). Organisms rely on regulatory networks to orchestrate the transcription of genes in response to internal or external environmental changes in order to optimize metabolism and enhance survival.…”
mentioning
confidence: 99%
“…Project (HMP; Mavromatis et al, 2009;Markowitz et al, 2010) to assess the coverage and abundance of these sequenced isolates or their close neighbors in saliva microbiota. The number of reads recruited by the 44 oral reference genomes represented merely 0.42% and 2.05% of the total non-human reads for the two sequenced samples (H114 and C201) respectively.…”
Section: Saliva Microbiomes Distinguish Caries-active Hosts F Yang Et Almentioning
confidence: 99%
“…not overlapping with zero and that had 430 per mil enrichment were considered. For analyses of marine bacterial genomic information, genomes of marine bacterial isolates were selected from the DOE Joint Genome Institute's Integrated Microbial Genomes (Markowitz et al, 2010) Database and gene annotation fields were searched for terms related to AA, FA and nucleoside transporters and extracellular nucleases. For phylogenetic relationships, the Greengenes 16S rRNA database (DeSantis et al, 2006) was imported into ARB (Ludwig et al, 2004) and all taxa except targets of the array analysis were removed with the taxon pruning function.…”
Section: Data Analysesmentioning
confidence: 99%