The integrated microbial genomes (IMG) system

Abstract

The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for analyzing genomes, genes and functions, individually or in a comparative context. IMG allows users to focus their analysis on subsets of genes and genomes of interest and to save the results of their analysis. IMG is available at http://img.jgi.doe.gov.

Figure 1

Gene Details Page and Gene Ortholog Neighborhoods. The gene neighborhood in the ‘Gene Details’ page shows the query gene (centered, in red) and other genes within a 25 kb window. A ‘Gene Ortholog Neighborhoods’ page shows the gene neighborhood of orthologs of the query gene, across several organisms. Each gene's neighborhood appears 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 with the same color indicate association with the same COG group. For each gene, locus tag, scaffold coordinates and COG group number are provided locally (by placing the cursor over the gene), while additional information is available in the Gene Details page that is linked to each gene.

Figure 2

Phylogenetic occurrence profile. The occurrence profiles of multiple genes across selected organisms can be visually compared. For each gene, a fixed length ordered vector is displayed in a BLAST-like alignment format. The positions in the vector correspond to the list of selected organisms, whereby the organisms are phylogenetically ordered; presence of a gene or its ortholog in a given organism is indicated by a domain letter (‘B’ for Bacteria, ‘A’ for Archaea and ‘E’ for Eukarya) while the absence of the gene is indicated by a dot (‘.’). One can mouse over the letter or dot to see the organism and phylum names.