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The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.

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

Bottom Line: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes.IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context.Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases.

View Article: PubMed Central - PubMed

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

ABSTRACT
The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all 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 annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.

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Related in: MedlinePlus

Profile search and functional profile tools. The ‘Phylogenetic Profiler’ tool is used to find genes in the archaeal genome Thermoplasma volcanium GSS1 (T. volcanium) that have no homologs in a phylogenetically closely related genome, Thermoplasma acidophilum DSM 1728 (T. acidophilum) (1). Similarity cutoffs are used to fine-tune the selection. The list of T. volcanium genes that satisfy the specified condition are provided as a list (2) from which genes can be selected and added to a Gene Cart. The ‘Abundance Profile Search’ tool is used to find COGs that are more abundant in T. volcanium than in T. acidophilum (3). The COGs that satisfy the specified condition are provided as a list (4) from which COGs can be selected and added to the Function Cart. For COGs of the ‘Signal transduction mechanisms’ in the Function Cart, the ‘Function Profile’ tool allows computing a profile across the T. volcanium and T. acidophilum genomes (5). The functional profile result is displayed as a matrix with each cell containing a link to the associated list of genes and displaying the count (abundance) of genes in this list. Colors are used to represent visually gene abundance, whereby white, bisque and yellow represent gene counts of 0, 1–4 and over 4, respectively (6). The T. volcanium and T. acidophilum genes associated with COG0467 are further examined with the ‘Gene Ortholog Neighborhoods’ tool (7): the compared genes are colored red, and their respective neighborhoods appear above and below a single line showing the genes reading in one direction on top and those reading in the opposite direction on the bottom; genes associated with the same color indicate association with the same COG group.
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Figure 1: Profile search and functional profile tools. The ‘Phylogenetic Profiler’ tool is used to find genes in the archaeal genome Thermoplasma volcanium GSS1 (T. volcanium) that have no homologs in a phylogenetically closely related genome, Thermoplasma acidophilum DSM 1728 (T. acidophilum) (1). Similarity cutoffs are used to fine-tune the selection. The list of T. volcanium genes that satisfy the specified condition are provided as a list (2) from which genes can be selected and added to a Gene Cart. The ‘Abundance Profile Search’ tool is used to find COGs that are more abundant in T. volcanium than in T. acidophilum (3). The COGs that satisfy the specified condition are provided as a list (4) from which COGs can be selected and added to the Function Cart. For COGs of the ‘Signal transduction mechanisms’ in the Function Cart, the ‘Function Profile’ tool allows computing a profile across the T. volcanium and T. acidophilum genomes (5). The functional profile result is displayed as a matrix with each cell containing a link to the associated list of genes and displaying the count (abundance) of genes in this list. Colors are used to represent visually gene abundance, whereby white, bisque and yellow represent gene counts of 0, 1–4 and over 4, respectively (6). The T. volcanium and T. acidophilum genes associated with COG0467 are further examined with the ‘Gene Ortholog Neighborhoods’ tool (7): the compared genes are colored red, and their respective neighborhoods appear above and below a single line showing the genes reading in one direction on top and those reading in the opposite direction on the bottom; genes associated with the same color indicate association with the same COG group.

Mentions: Genomes can be compared in terms of gene content using the ‘Phylogenetic Profiler’ tool that allows to define a ‘profile’ for the genes of the query genome, say the archaeal genome Thermoplasma volcanium GSS1 (T. volcanium) in terms of presence or absence of homologs in any other genomes. In the example shown in pane (1) of Figure 1, the tool is used to find T. volcanium genes that have no homologs in Thermoplasma acidophilum DSM 1728 (T. acidophilum). Similarity cutoffs can be used to fine-tune the selection. The list of genes with the specified profile are then provided as a selectable list as shown in pane (2) of Figure 1. The ‘Phylogenetic Profiler’ tool can be used, e.g. for finding ‘unique’ genes in the query genome with respect to other genomes of interest. In the example shown in Figure 1, 241 genes are found to be unique in T. volcanium with respect to T. acidophilum.Figure 1.


The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.

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

Profile search and functional profile tools. The ‘Phylogenetic Profiler’ tool is used to find genes in the archaeal genome Thermoplasma volcanium GSS1 (T. volcanium) that have no homologs in a phylogenetically closely related genome, Thermoplasma acidophilum DSM 1728 (T. acidophilum) (1). Similarity cutoffs are used to fine-tune the selection. The list of T. volcanium genes that satisfy the specified condition are provided as a list (2) from which genes can be selected and added to a Gene Cart. The ‘Abundance Profile Search’ tool is used to find COGs that are more abundant in T. volcanium than in T. acidophilum (3). The COGs that satisfy the specified condition are provided as a list (4) from which COGs can be selected and added to the Function Cart. For COGs of the ‘Signal transduction mechanisms’ in the Function Cart, the ‘Function Profile’ tool allows computing a profile across the T. volcanium and T. acidophilum genomes (5). The functional profile result is displayed as a matrix with each cell containing a link to the associated list of genes and displaying the count (abundance) of genes in this list. Colors are used to represent visually gene abundance, whereby white, bisque and yellow represent gene counts of 0, 1–4 and over 4, respectively (6). The T. volcanium and T. acidophilum genes associated with COG0467 are further examined with the ‘Gene Ortholog Neighborhoods’ tool (7): the compared genes are colored red, and their respective neighborhoods appear above and below a single line showing the genes reading in one direction on top and those reading in the opposite direction on the bottom; genes associated with the same color indicate association with the same COG group.
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Related In: Results  -  Collection

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Figure 1: Profile search and functional profile tools. The ‘Phylogenetic Profiler’ tool is used to find genes in the archaeal genome Thermoplasma volcanium GSS1 (T. volcanium) that have no homologs in a phylogenetically closely related genome, Thermoplasma acidophilum DSM 1728 (T. acidophilum) (1). Similarity cutoffs are used to fine-tune the selection. The list of T. volcanium genes that satisfy the specified condition are provided as a list (2) from which genes can be selected and added to a Gene Cart. The ‘Abundance Profile Search’ tool is used to find COGs that are more abundant in T. volcanium than in T. acidophilum (3). The COGs that satisfy the specified condition are provided as a list (4) from which COGs can be selected and added to the Function Cart. For COGs of the ‘Signal transduction mechanisms’ in the Function Cart, the ‘Function Profile’ tool allows computing a profile across the T. volcanium and T. acidophilum genomes (5). The functional profile result is displayed as a matrix with each cell containing a link to the associated list of genes and displaying the count (abundance) of genes in this list. Colors are used to represent visually gene abundance, whereby white, bisque and yellow represent gene counts of 0, 1–4 and over 4, respectively (6). The T. volcanium and T. acidophilum genes associated with COG0467 are further examined with the ‘Gene Ortholog Neighborhoods’ tool (7): the compared genes are colored red, and their respective neighborhoods appear above and below a single line showing the genes reading in one direction on top and those reading in the opposite direction on the bottom; genes associated with the same color indicate association with the same COG group.
Mentions: Genomes can be compared in terms of gene content using the ‘Phylogenetic Profiler’ tool that allows to define a ‘profile’ for the genes of the query genome, say the archaeal genome Thermoplasma volcanium GSS1 (T. volcanium) in terms of presence or absence of homologs in any other genomes. In the example shown in pane (1) of Figure 1, the tool is used to find T. volcanium genes that have no homologs in Thermoplasma acidophilum DSM 1728 (T. acidophilum). Similarity cutoffs can be used to fine-tune the selection. The list of genes with the specified profile are then provided as a selectable list as shown in pane (2) of Figure 1. The ‘Phylogenetic Profiler’ tool can be used, e.g. for finding ‘unique’ genes in the query genome with respect to other genomes of interest. In the example shown in Figure 1, 241 genes are found to be unique in T. volcanium with respect to T. acidophilum.Figure 1.

Bottom Line: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes.IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context.Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases.

View Article: PubMed Central - PubMed

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

ABSTRACT
The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all 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 annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.

Show MeSH
Related in: MedlinePlus