Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

BMC Bioinformatics

Research

Paul Rupek¹  Daniel H Huson¹  Suparna Mitra¹  Daniel C Richter²  Jack A Gilbert³  Tim Urich⁴  Andreas Wilke⁵  Folker Meyer⁵ 

[1] Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076, Tübingen, Germany;Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076, Tübingen, Germany;Eurofins Medigenomix GmbH, Anzinger Str. 7, 85560, Ebersberg, Germany;Department of Ecology and Evolution, The University of Chicago, 60637, Chicago, IL, USA;Mathematics and Computer Science Division, Argonne National Laboratory, 60439, Argonne, IL, USA;Department of Genetics in Ecology, Vienna Ecology Center, University of Vienna, 1090, Vienna, Austria;Centre for Geobiology, University of Bergen, 5007, Bergen, Norway;Mathematics and Computer Science Division, Argonne National Laboratory, 60439, Argonne, IL, USA;

关键词: Microbial Community;    Pathway Analysis;    Multiple Dataset;    Functional Assignment;    NCBI Taxonomy;   

DOI  :  10.1186/1471-2105-12-S1-S21

来源: Springer

【 摘 要 】

BackgroundMetagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the number and scope of metagenome projects. While metagenomics provides information on the gene content, metatranscriptomics aims at understanding gene expression patterns in microbial communities. The initial computational analysis of a metagenome or metatranscriptome addresses three questions: (1) Who is out there? (2) What are they doing? and (3) How do different datasets compare? There is a need for new computational tools to answer these questions. In 2007, the program MEGAN (MEtaGenome ANalyzer) was released, as a standalone interactive tool for analyzing the taxonomic content of a single metagenome dataset. The program has subsequently been extended to support comparative analyses of multiple datasets.ResultsThe focus of this paper is to report on new features of MEGAN that allow the functional analysis of multiple metagenomes (and metatranscriptomes) based on the SEED hierarchy and KEGG pathways. We have compared our results with the MG-RAST service for different datasets.ConclusionsThe MEGAN program now allows the interactive analysis and comparison of the taxonomical and functional content of multiple datasets. As a stand-alone tool, MEGAN provides an alternative to web portals for scientists that have concerns about uploading their unpublished data to a website.

【 授权许可】

CC BY   
© Mitra et al; licensee BioMed Central Ltd. 2011