METAGENassist: a comprehensive web server for comparative metagenomics.
METAGENassist: a comprehensive web server for comparative metagenomics.
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DOI：
10.1093/nar/gks497
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发表时间：
2012-07
影响因子：
14.9
通讯作者：
Wishart DS
中科院分区：
文献类型：
--
作者：
Arndt D;Xia J;Liu Y;Zhou Y;Guo AC;Cruz JA;Sinelnikov I;Budwill K;Nesbø CL;Wishart DS
随着DNA测序和样本提取技术的最近改进，元基因组数据的数量和质量现在呈指数级增长。这些丰富的注释丰富的元基因组数据和细菌普查信息催生了微生物学的一个新分支，称为比较元基因组学。比较元基因组学涉及不同环境样本、不同培养条件或不同微生物宿主之间的细菌种群比较。然而，为了进行比较元基因组学，人们通常需要掌握多变量统计的复杂知识和/或高级软件编程技能。为了使微生物学家更容易获得比较元基因组学，我们开发了一个免费访问、易于使用的Web服务器，用于比较元基因组分析，称为METAGENAssist.用户可以从各种常见格式上传他们的细菌普查数据，使用扩增的16S rRNA数据或鸟枪式元基因组数据。还可以上载关于环境、文化或宿主条件的元数据。在数据上传过程中，METAGENAssistate还执行自动分类到表型的映射。从分类输入数据自动生成涵盖近20个功能类别的表型信息，如GC含量、基因组大小、氧气需求、能源和首选温度范围。使用这种表型丰富的数据，用户然后可以执行各种多变量和单变量数据分析，包括折叠变化分析、t检验、主成分分析、偏最小二乘法、聚类和分类。为了便于数据处理，使用各种菜单、信息超链接和复选框引导用户逐步完成分析工作流程。METAGENASSITE还可以生成彩色的出版质量表格和图表，可以下载并直接用于科学论文的准备。METAGENASSIST的网址是：http://www.metagenassist.ca.
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.
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影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
5.8
作者：
Parks, Donovan H.;Beiko, Robert G.
通讯作者：
Beiko, Robert G.
影响因子：
4.3
作者：
White JR;Nagarajan N;Pop M
通讯作者：
Pop M
影响因子：
4.4
作者：
Schloss, Patrick D.;Westcott, Sarah L.;Weber, Carolyn F.
通讯作者：
Weber, Carolyn F.
影响因子：
46.9
作者：
Noble, William S.
通讯作者：
Noble, William S.