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

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.

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.

Figure 2.

MyIMG user annotations. A gene of P. furiosus (with the object identifier ‘638173757’) is associated with product name NADH oxidase, as displayed by its ‘Gene Details’ page (1), and as recorded in GenBank and RefSeq, which can be viewed by following the appropriate External Links. For gene ‘638173757’, one can display its list of orthologs, which can be accessed in the Homologs section of its ‘Gene Details page (2). The top three orthologs of gene ‘638173757’ can be selected and saved together with the gene into the Gene Cart, where the product name is changed to NADPH:sulfur oxidoreductas with the ‘MyIMG Annotation’ tool (3). Other annotations (e.g. EC number) can be also modified. User annotations can be subsequently reviewed, imported into IMG from a user file, or exported to a user file using ‘My Annotations’ page (4).