1. Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System 
Victor M. Markowitz, I-Min A. Chen, Ken Chu, Amrita Pati, Natalia N. Ivanova, Nikos C. Kyrpides 
Trends in Microbiology 
Volume 23, Issue 11, Pages (November 2015)
DOI: /j.tim
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2. Figure 1 IMG Content History.
Trends in Microbiology  , DOI: ( /j.tim )
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3. Figure 2
IMG Analysis Tools Organization. (i) Genomes, metagenomes, genes, and functions can be selected using browsers and search tools, then examined individually or using (ii) comparative analysis tools. The results of individual analysis steps can be preserved during an analysis session using (iii) genome, scaffold, gene, and function specific ‘carts’, or by saving the results as persistent sets using (iv) IMG's workspace. Users can revise the gene annotations for their ‘private’ datasets in IMG, which can then be reviewed via MyIMG's Annotations (iv).
Trends in Microbiology  , DOI: ( /j.tim )
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4. Figure 3
Data Exploration Use Case. (i) Metagenome datasets can be examined using the Microbiome Details page, which provides tools for browsing, searching, or downloading the metagenome data. (ii) Scaffold Cart allows selecting individual scaffolds or groups of scaffolds based on properties such as gene content. (iii) The Phylogenetic Distribution of Genes provides an estimate of the phylogenetic composition of a metagenome sample based on the distribution of the best BLAST hits of the protein-coding genes in the sample, with the result displayed using (iv) the Radial Tree viewer or (v) in a tabular format consisting 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). (vi) The organization of genes by their assignment to COGs can be displayed in a pie chart format.
Trends in Microbiology  , DOI: ( /j.tim )
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5. Figure 4
Comparative Analysis Tools Use Case. (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 KO terms. (Meta)genome datasets can be selected for comparison, with the result displayed in (iii) the context of the KEGG pathway map, with each enzyme number on the map colored depending on the percentage of genomes with a gene associated with that enzyme. (iv) (Meta)genome datasets of interest can be also compared in terms of the relative abundance of all/a subset of protein families, functional families (enzymes), or functional categories (such as KEGG Orthology terms).
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6. Figure 5
Workspace Sets and Computation. (i) Metagenome and genome datasets, genes, functions, and scaffolds of interest can be saved as persistent sets in a user-specific Workspace. Such sets can be manipulated using set operations (ii), or can be part of function comparisons (iii). Long-running analysis operations can be submitted for offline processing as background computations, with the status provided via the MyJob section of MyIMG's menu option (iv). When a computation is completed, links are provided for accessing the analysis results.
Trends in Microbiology  , DOI: ( /j.tim )
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