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. 2021 Jan 8;49(D1):D751-D763.
doi: 10.1093/nar/gkaa939.

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities

I-Min A Chen  1 , Ken Chu  1 , Krishnaveni Palaniappan  1 , Anna Ratner  1 , Jinghua Huang  1 , Marcel Huntemann  1 , Patrick Hajek  1 , Stephan Ritter  1 , Neha Varghese  1 , Rekha Seshadri  1 , Simon Roux  1 , Tanja Woyke  1 , Emiley A Eloe-Fadrosh  1 , Natalia N Ivanova  1 , Nikos C Kyrpides  1
Affiliations

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities

I-Min A Chen et al. Nucleic Acids Res. .

Abstract

The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) contains annotated isolate genome and metagenome datasets sequenced at the DOE's Joint Genome Institute (JGI), submitted by external users, or imported from public sources such as NCBI. IMG v 6.0 includes advanced search functions and a new tool for statistical analysis of mixed sets of genomes and metagenome bins. The new IMG web user interface also has a new Help page with additional documentation and webinar tutorials to help users better understand how to use various IMG functions and tools for their research. New datasets have been processed with the prokaryotic annotation pipeline v.5, which includes extended protein family assignments.

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Figures

Figure 1.
Figure 1.
Gene Search. (A) The Find Genes menu includes the new Gene Search function and BLAST. (B) Quick search allows users to search genes using function IDs such as pfam00698 or using names. (C) Quick search result of pfam00698 shows the numbers of genes and genomes with this particular function.
Figure 2.
Figure 2.
Advanced Search Builder option for the new Gene Search feature. (A) The advanced search option allows users to search all 16s rRNA genes with length greater than 500nt in the freshwater sediment metagenomes previously saved in the Genome Cart. (B) The search result shows that there are 131 genes satisfying the search criteria. (C) Users can view and reuse previously constructed query conditions.
Figure 3.
Figure 3.
Browse metagenome bins by Ecosystem. (A) From the Find Genomes menu item, users can select Metagenome Bins to find Bins by Ecosystem browse option. (B) Users can click on any cell to expand. This example shows the expansion of Plants ecosystem category under Host-associated ecosystem. (C) Users can click on the ‘breadcrumb’ to view the detailed list. (D) The list shows all metagenome bins in the Nodule ecosystem type. Users can select any or all of the six bins to add to the scaffold analysis cart or workspace scaffold dataset.
Figure 4.
Figure 4.
Advanced Search Builder option of the new Metagenome Bin Search feature. (A) The Bin Search option in metagenome bin search allows users to search all metagenome bins in the IMG database using quick search or advanced search. (B) Users can build a complex query to find Butyrivibrio and Pseudobutyrivibrio bins with completeness of at least 90% and in no more than 180 contigs or scaffolds. Users can click the Search button to run the query. (C) Result shows that 11 bins satisfying this query condition. (Only 3 rows are displayed here.)
Figure 5.
Figure 5.
New analysis tool for users to analyze genomes together with metagenome bins. (A) In the Workspace, a user can create new Analysis Data Groups (ADGs) by dragging and dropping genome sets and scaffold sets. A new ADG butyrivibrio_bin_group is created to include all the 10 butyrivibrio metagenome bins. (B) Two additional ADGs enolase_positive_group and enolase_negative_group can be created to include genome sets enolase_positive_butyrivibrio and enolase_negative_butyrivibrio, respectively. (C) The user can then select the three ADGs to analyze Pfam distribution using the suggested analysis method, and submit the statistical analysis to be a computation job. (D) The user will receive an email notification when the job has been completed. The result can be viewed following the link included in the email or from a corresponding link in the Workspace My Jobs list.
Figure 6.
Figure 6.
New Help Page: We have redesigned the IMG Help page to help users to better understand the system.
See this image and copyright information in PMC

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