Integrative analysis of environmental sequences using MEGAN4

被引：1162

作者：

Huson, Daniel H. ^{[1
]}

Mitra, Suparna ^{[1
]}

Ruscheweyh, Hans-Joachim ^{[1
]}

Weber, Nico ^{[1
]}

Schuster, Stephan C. ^{[2
]}

机构：

[1] Univ Tubingen, Ctr Bioinformat, D-72076 Tubingen, Germany

[2] Penn State Univ, Ctr Comparat Genom, University Pk, PA 16802 USA

来源：

GENOME RESEARCH | 2011年 / 21卷 / 09期

关键词：

PHYLOGENETIC CLASSIFICATION; ENCYCLOPEDIA; METAGENOMICS; MICROBIOME; RESOURCE; PROJECT;

D O I：

10.1101/gr.120618.111

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

引用

页码：1552 / 1560

页数：9

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