METAGENassist: a comprehensive web server for comparative metagenomics
With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative me...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394294/ https://www.ncbi.nlm.nih.gov/pubmed/22645318 http://dx.doi.org/10.1093/nar/gks497 |
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author | Arndt, David Xia, Jianguo Liu, Yifeng Zhou, You Guo, An Chi Cruz, Joseph A. Sinelnikov, Igor Budwill, Karen Nesbø, Camilla L. Wishart, David S. |
author_facet | Arndt, David Xia, Jianguo Liu, Yifeng Zhou, You Guo, An Chi Cruz, Joseph A. Sinelnikov, Igor Budwill, Karen Nesbø, Camilla L. Wishart, David S. |
author_sort | Arndt, David |
collection | PubMed |
description | With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative metagenomics. Comparative metagenomics involves the comparison of bacterial populations between different environmental samples, different culture conditions or different microbial hosts. However, in order to do comparative metagenomics, one typically requires a sophisticated knowledge of multivariate statistics and/or advanced software programming skills. To make comparative metagenomics more accessible to microbiologists, we have developed a freely accessible, easy-to-use web server for comparative metagenomic analysis called METAGENassist. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data. Metadata concerning environmental, culture, or host conditions can also be uploaded. During the data upload process, METAGENassist also performs an automated taxonomic-to-phenotypic mapping. Phenotypic information covering nearly 20 functional categories such as GC content, genome size, oxygen requirements, energy sources and preferred temperature range is automatically generated from the taxonomic input data. Using this phenotypically enriched data, users can then perform a variety of multivariate and univariate data analyses including fold change analysis, t-tests, PCA, PLS-DA, clustering and classification. To facilitate data processing, users are guided through a step-by-step analysis workflow using a variety of menus, information hyperlinks and check boxes. METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca. |
format | Online Article Text |
id | pubmed-3394294 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-33942942012-07-30 METAGENassist: a comprehensive web server for comparative metagenomics Arndt, David Xia, Jianguo Liu, Yifeng Zhou, You Guo, An Chi Cruz, Joseph A. Sinelnikov, Igor Budwill, Karen Nesbø, Camilla L. Wishart, David S. Nucleic Acids Res Articles With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative metagenomics. Comparative metagenomics involves the comparison of bacterial populations between different environmental samples, different culture conditions or different microbial hosts. However, in order to do comparative metagenomics, one typically requires a sophisticated knowledge of multivariate statistics and/or advanced software programming skills. To make comparative metagenomics more accessible to microbiologists, we have developed a freely accessible, easy-to-use web server for comparative metagenomic analysis called METAGENassist. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data. Metadata concerning environmental, culture, or host conditions can also be uploaded. During the data upload process, METAGENassist also performs an automated taxonomic-to-phenotypic mapping. Phenotypic information covering nearly 20 functional categories such as GC content, genome size, oxygen requirements, energy sources and preferred temperature range is automatically generated from the taxonomic input data. Using this phenotypically enriched data, users can then perform a variety of multivariate and univariate data analyses including fold change analysis, t-tests, PCA, PLS-DA, clustering and classification. To facilitate data processing, users are guided through a step-by-step analysis workflow using a variety of menus, information hyperlinks and check boxes. METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca. Oxford University Press 2012-07 2012-05-29 /pmc/articles/PMC3394294/ /pubmed/22645318 http://dx.doi.org/10.1093/nar/gks497 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Arndt, David Xia, Jianguo Liu, Yifeng Zhou, You Guo, An Chi Cruz, Joseph A. Sinelnikov, Igor Budwill, Karen Nesbø, Camilla L. Wishart, David S. METAGENassist: a comprehensive web server for comparative metagenomics |
title | METAGENassist: a comprehensive web server for comparative metagenomics |
title_full | METAGENassist: a comprehensive web server for comparative metagenomics |
title_fullStr | METAGENassist: a comprehensive web server for comparative metagenomics |
title_full_unstemmed | METAGENassist: a comprehensive web server for comparative metagenomics |
title_short | METAGENassist: a comprehensive web server for comparative metagenomics |
title_sort | metagenassist: a comprehensive web server for comparative metagenomics |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394294/ https://www.ncbi.nlm.nih.gov/pubmed/22645318 http://dx.doi.org/10.1093/nar/gks497 |
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