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. 2012;7(7):e40151.
doi: 10.1371/journal.pone.0040151. Epub 2012 Jul 5.

IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project

Victor M Markowitz  1 , I-Min A Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Biju Jacob, Anna Ratner, Konstantinos Liolios, Ioanna Pagani, Marcel Huntemann, Konstantinos Mavromatis, Natalia N Ivanova, Nikos C Kyrpides
Affiliations

IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project

Victor M Markowitz et al. PLoS One. 2012.

Abstract

The Integrated Microbial Genomes and Metagenomes (IMG/M) resource is a data management system that supports the analysis of sequence data from microbial communities in the integrated context of all publicly available draft and complete genomes from the three domains of life as well as a large number of plasmids and viruses. IMG/M currently contains thousands of genomes and metagenome samples with billions of genes. IMG/M-HMP is an IMG/M data mart serving the US National Institutes of Health (NIH) Human Microbiome Project (HMP), focussed on HMP generated metagenome datasets, and is one of the central resources provided from the HMP Data Analysis and Coordination Center (DACC). IMG/M-HMP is available at http://www.hmpdacc-resources.org/imgm_hmp/.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Grouping and Classification of metagenome datasets in IMG/M HMP.
Figure 2
Figure 2. Distribution of genes of microbiomes grouped taxonomically and by habitat according to their best BLASTp hit to reference genomes.
Figure 3
Figure 3. Metagenome comparison tools in IMG/M-HMP.
(i) The metagenome comparison tool menu in IMG/M-HMP; (ii) Genome Clustering tool menu in IMG/M-HMP; (iii) Principal Component Analysis (PCA) plot for all stool samples using COGs showing the outlier samples; (iv) Function Comparisons tool menu in IMG/M-HMP; (v) Function Comparisons tool results using an outlier from (iii) - metagenome of stool sample of subject 160158126, visit 1 - as a query and several outlier and non-outlier samples as references.
Figure 4
Figure 4. Estimation of metagenome composition using Phylogenetic Distribution tool in IMG/M-HMP.
(i) Navigation to Phylogenetic Distribution tool in Compare Genomes menu in IMG/M-HMP; (ii) results of Phylogenetic Distribution comparison displayed in tabular format for one outlier sample - metagenome of stool sample of subject 160158126, visit 1– and several non-outlier samples; (iii) results of Phylogenetic Distribution comparison displayed as a bar chart with pink bars corresponding to the metagenome of stool sample of subject 160158126, visit 1.
See this image and copyright information in PMC

References

    1. Mavromatis K, Ivanova NN, Anderson I, Huntemann M, Williams P, et al. The DOE-JGI standard operating procedure for the annotations of metagenomes. Submitted for publication to SIGS. 2011. ( http://standardsingenomics.org/).
    1. Markowitz VM, Chen IMA, Chu K, Szeto E, Palaniappan K, et al. IMG/M: the integrated metagenome data management and comparative analysis system, Nucleic Acid Res. 2012. - PMC - PubMed
    1. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, et al. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007;8:209. - PMC - PubMed
    1. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–964. - PMC - PubMed
    1. Hyatt D, Che GL, LoCascio PF, Land ML, Larimer FW, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics. 2010;11:119. - PMC - PubMed

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