IMG/M 4 version of the integrated metagenome comparative analysis system

Abstract

IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M's data content and analytical tools have expanded continuously since its first version was released in 2007. Since the last report published in the 2012 NAR Database Issue, IMG/M's database architecture, annotation and data integration pipelines and analysis tools have been extended to copewith the rapid growth in the number and size of metagenome data sets handled by the system. IMG/M data marts provide support for the analysis of publicly available genomes, expert review of metagenome annotations (IMG/M ER: http://img.jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/imgm_hmp).

Figure 1.

RNA-Seq data organization. (i) Metatranscriptomic (RNA-Seq) data sets can be accessed from ‘IMG Statistics’ on IMG/M’s front page, following the experiments link available on the ‘IMG Statistics’ page. (ii) An RNA-Seq study is associated with a metagenome project (assembly onto which the RNA-Seq reads have been mapped) and a number of samples. (iii) RNA-Seq studies associated with a metagenome project can be accessed from its ‘Microbiome Details’, with each study associated with (iv) a list of RNA-Seq experiments (samples). Individual samples can be selected for further analysis, such as (v) examining its expressed genes as a list.

Figure 2.

Using workspace tools to analyze metagenome samples. (i) ‘Workspace’ is part of the ‘MyIMG’ toolkit and consists of user-specified ‘Gene Sets’, ‘Genome Sets’, ‘Function Sets’ and ‘Scaffold Sets’, which can be created by (ii) transferring objects from the corresponding ‘Carts’ or from the lists of objects retrieved by IMG analysis tools, such as similarity searches or ‘Phylogenetic Distribution of Genes’. (iii) ‘Workspace’ supports profile operations between different sets of objects, with (iv) the results used to define new sets of genes and functions. (v) ‘Workspace’ operations on sets of objects include union, intersection and subtraction, with the results saved as new sets of objects.

Figure 3.

Background computations support analysis involving large sets of genes, functions and scaffolds, which can be specified using ‘Workspace’ (i) ‘Gene Sets’, (ii) ‘Function Sets’ and ‘Scaffold Sets’. Thus, (iii) a ‘Function Profile’ can be submitted as a background computation, whereby (iv) its status can be checked with ‘MyJob’. (v) For completed computations links are provided for accessing the analysis results, and (vii) associated details.