IMG: the Integrated Microbial Genomes database and comparative analysis system

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 integrates publicly available draft and complete genomes from all three domains of life 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. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp).

Figure 1.

A sample of rules for predicting phenotypes in IMG.

Figure 2.

Genome browser and search tools. The ‘Genome Browser’ displays the genomes organized in a phylogenetic tree or (i) in a tabular list that can be configured by (ii) adding or removing genome, metadata or annotation specific columns. (iii) ‘Genome Search’ allows searching genomes on genome or metadata specific fields. (iv) A genome can be explored using a variety of browsing tools, searched for the presence of specific genes using BLAST, or downloaded.

Figure 3.

Protein expression exploration tools. (i) ‘Protein Expression Studies’ are listed on the IMG Statistics page, with each study associated with (ii) a list of ‘Protein Expression Experiments’ (samples). (iii) Samples can be selected for further analysis, such as examining expressed genes of (iv) a single sample in the context of pathway, where enzymes are displayed with colours representing the level of expression for the associated genes. (v) Sample pairs can be compared in terms of genes up or down regulation, with the result of the comparison displayed as a histogram.

Figure 4.

Comparative analysis tools. (i) A pathway is selected from the list of KEGG pathways via the KEGG option of the ‘Find Functions’ menu, and subsequently (ii) the ‘KEGG Pathway Details’ lists its associated enzymes and the list of genomes organized phylogenetically. (iii) Once genomes are selected for comparison, the result is displayed in the context of the KEGG pathway map, with each enzyme number on the map coloured depending on the percentage of genomes with a gene associated with that enzyme. (iv) The ‘Radial Phylogenetic Tree’ is one of several tools provided for comparing genomes, and (v) allows comparing the BLAST hits of the genes of up to five user selected genomes to the genes of all the genomes in the database using a colour-coded hierarchical circular tree viewer.