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

Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.

ABSTRACT
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.

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Related in: MedlinePlus

Metagenome Data Exploration and Visualization Tools. Individual microbiome samples such as the ‘Sludge/Australian’ sample, can be examined using the ‘Microbiome Details’ page, which includes relevant microbiome information (1). The ‘Phylogenetic Distribution of Genes’ tool (2) displays the distribution of best BLAST hits of protein-coding genes in the microbiome as a histogram, with counts of genes that have best BLASTp hits to proteins of isolate genomes in each phylum or class with more than 90% identity, 60–90% identity and 30–60% identity. The distribution of genes for each phylum/class can be projected onto the families in that phylum/class such as Betaproteobacteria, and then further projected onto the species in that family such as Rhodocyclaceae. The genes in the sample can be viewed in the context of an individual reference isolate genome such as Dechloromonas aromatica, using the ‘Reference Genome Context Viewer’ (3), or using a ‘Protein Recruitment Plot’ (4). For each gene on ‘Reference Genome Context Viewer’ and ‘Protein Recruitment Plot’, locus tag and scaffold coordinates are provided locally (by placing the cursor over the gene), while additional information is available in the ‘Gene Details’ page, which is linked to each gene.
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Figure 1: Metagenome Data Exploration and Visualization Tools. Individual microbiome samples such as the ‘Sludge/Australian’ sample, can be examined using the ‘Microbiome Details’ page, which includes relevant microbiome information (1). The ‘Phylogenetic Distribution of Genes’ tool (2) displays the distribution of best BLAST hits of protein-coding genes in the microbiome as a histogram, with counts of genes that have best BLASTp hits to proteins of isolate genomes in each phylum or class with more than 90% identity, 60–90% identity and 30–60% identity. The distribution of genes for each phylum/class can be projected onto the families in that phylum/class such as Betaproteobacteria, and then further projected onto the species in that family such as Rhodocyclaceae. The genes in the sample can be viewed in the context of an individual reference isolate genome such as Dechloromonas aromatica, using the ‘Reference Genome Context Viewer’ (3), or using a ‘Protein Recruitment Plot’ (4). For each gene on ‘Reference Genome Context Viewer’ and ‘Protein Recruitment Plot’, locus tag and scaffold coordinates are provided locally (by placing the cursor over the gene), while additional information is available in the ‘Gene Details’ page, which is linked to each gene.

Mentions: Metagenomes and isolate genomes can be selected using a keyword based ‘Genome Search’ tool or a ‘Genome Browser’. Microbiomes can be further examined using the ‘Microbiome Details’, where a user can find relevant metadata such as sample site, as shown in pane 1 of Figure 1, along with various summaries of interest such as the total number of scaffolds and genes or the number of genes associated with functional characterizations (e.g. COG, Pfam). The ‘Phylogenetic Distribution of Genes’, shown in pane 2 of Figure 1, provides an estimate of the phylogenetic composition of a microbiome sample based on the distribution of the best BLAST hits of the protein-coding genes in the sample. The ‘Phylogenetic Distribution of Genes’ consists of a histogram, with counts of protein-coding genes in the sample that have best BLASTp hits to proteins of isolate genomes in each phylum or class with more than 90% identity (right column), 60–90% identity (middle column) and 30–60% identity (left column). The higher the number of hits and percent identity cutoff, the more likely it is that the sample contains close relatives of the sequenced isolate genomes from this phylum/class. Gene counts in the histogram are linked to the corresponding lists of genes, which can then be selected and added to ‘Gene Cart’ or analyzed through their ‘Gene Pages’. For each phylum/class, the phylogenetic distribution of genes can be projected onto the families in that phylum/class; for each family the distribution of genes can be further projected onto the species in that family. Finally, the genes in the sample can be viewed in the context of an individual reference isolate genome, using either the ‘Reference Genome Context Viewer’ as shown in pane 3 of Figure 1, or the ‘Protein Recruitment Plot’, as shown in pane 4 of Figure 1. The ‘Reference Genome Context Viewer’ displays the metagenome genes aligned with their homologous genes of the reference isolate genome. The metagenome genes are color coded to indicate BLAST percent identity (blue for 30%, green for 60% and red for 90%), while the genes of the reference genome are color coded to indicate their COG functional role, and are displayed as they are located along the chromosome. The ‘Protein Recruitment Plot’ displays the BLASTp hits of the metagenome genes against the genes of the reference genome, with the coordinates of the scaffold reference genome and the BLAST percent identities shown on the X and Y axis, respectively.Figure 1.


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

Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC - Nucleic Acids Res. (2007)

Metagenome Data Exploration and Visualization Tools. Individual microbiome samples such as the ‘Sludge/Australian’ sample, can be examined using the ‘Microbiome Details’ page, which includes relevant microbiome information (1). The ‘Phylogenetic Distribution of Genes’ tool (2) displays the distribution of best BLAST hits of protein-coding genes in the microbiome as a histogram, with counts of genes that have best BLASTp hits to proteins of isolate genomes in each phylum or class with more than 90% identity, 60–90% identity and 30–60% identity. The distribution of genes for each phylum/class can be projected onto the families in that phylum/class such as Betaproteobacteria, and then further projected onto the species in that family such as Rhodocyclaceae. The genes in the sample can be viewed in the context of an individual reference isolate genome such as Dechloromonas aromatica, using the ‘Reference Genome Context Viewer’ (3), or using a ‘Protein Recruitment Plot’ (4). For each gene on ‘Reference Genome Context Viewer’ and ‘Protein Recruitment Plot’, locus tag and scaffold coordinates are provided locally (by placing the cursor over the gene), while additional information is available in the ‘Gene Details’ page, which is linked to each gene.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238950&req=5

Figure 1: Metagenome Data Exploration and Visualization Tools. Individual microbiome samples such as the ‘Sludge/Australian’ sample, can be examined using the ‘Microbiome Details’ page, which includes relevant microbiome information (1). The ‘Phylogenetic Distribution of Genes’ tool (2) displays the distribution of best BLAST hits of protein-coding genes in the microbiome as a histogram, with counts of genes that have best BLASTp hits to proteins of isolate genomes in each phylum or class with more than 90% identity, 60–90% identity and 30–60% identity. The distribution of genes for each phylum/class can be projected onto the families in that phylum/class such as Betaproteobacteria, and then further projected onto the species in that family such as Rhodocyclaceae. The genes in the sample can be viewed in the context of an individual reference isolate genome such as Dechloromonas aromatica, using the ‘Reference Genome Context Viewer’ (3), or using a ‘Protein Recruitment Plot’ (4). For each gene on ‘Reference Genome Context Viewer’ and ‘Protein Recruitment Plot’, locus tag and scaffold coordinates are provided locally (by placing the cursor over the gene), while additional information is available in the ‘Gene Details’ page, which is linked to each gene.
Mentions: Metagenomes and isolate genomes can be selected using a keyword based ‘Genome Search’ tool or a ‘Genome Browser’. Microbiomes can be further examined using the ‘Microbiome Details’, where a user can find relevant metadata such as sample site, as shown in pane 1 of Figure 1, along with various summaries of interest such as the total number of scaffolds and genes or the number of genes associated with functional characterizations (e.g. COG, Pfam). The ‘Phylogenetic Distribution of Genes’, shown in pane 2 of Figure 1, provides an estimate of the phylogenetic composition of a microbiome sample based on the distribution of the best BLAST hits of the protein-coding genes in the sample. The ‘Phylogenetic Distribution of Genes’ consists of a histogram, with counts of protein-coding genes in the sample that have best BLASTp hits to proteins of isolate genomes in each phylum or class with more than 90% identity (right column), 60–90% identity (middle column) and 30–60% identity (left column). The higher the number of hits and percent identity cutoff, the more likely it is that the sample contains close relatives of the sequenced isolate genomes from this phylum/class. Gene counts in the histogram are linked to the corresponding lists of genes, which can then be selected and added to ‘Gene Cart’ or analyzed through their ‘Gene Pages’. For each phylum/class, the phylogenetic distribution of genes can be projected onto the families in that phylum/class; for each family the distribution of genes can be further projected onto the species in that family. Finally, the genes in the sample can be viewed in the context of an individual reference isolate genome, using either the ‘Reference Genome Context Viewer’ as shown in pane 3 of Figure 1, or the ‘Protein Recruitment Plot’, as shown in pane 4 of Figure 1. The ‘Reference Genome Context Viewer’ displays the metagenome genes aligned with their homologous genes of the reference isolate genome. The metagenome genes are color coded to indicate BLAST percent identity (blue for 30%, green for 60% and red for 90%), while the genes of the reference genome are color coded to indicate their COG functional role, and are displayed as they are located along the chromosome. The ‘Protein Recruitment Plot’ displays the BLASTp hits of the metagenome genes against the genes of the reference genome, with the coordinates of the scaffold reference genome and the BLAST percent identities shown on the X and Y axis, respectively.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus