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Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.

Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH - BMC Bioinformatics (2011)

Bottom Line: We have compared our results with the MG-RAST service for different datasets.The 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stand-alone tool, MEGAN provides an alternative to web portals for scientists that have concerns about uploading their unpublished data to a website.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076 Tübingen, Germany. mitra@informatik.uni-tuebingen.de.

ABSTRACT

Background: Metagenomics 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.

Results: The 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.

Conclusions: The 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stand-alone tool, MEGAN provides an alternative to web portals for scientists that have concerns about uploading their unpublished data to a website.

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SEED-based functional comparison. Part of a SEED-based functional comparison of eight marine samples.
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Figure 2: SEED-based functional comparison. Part of a SEED-based functional comparison of eight marine samples.

Mentions: MEGAN supports the simultaneous analysis and comparison of the taxonomic content and now also the functional content of multiple datasets in several ways. The functional content of a set of metagenomes can be simulteniously opened and compared using a new SEED-based tree view (see Figure 2). Furthermore a collection of datasets can be compared using six different ecological indices, the UniFrac measure [2] and different distance analysis techniques (see [14] for details). As an example Figure 3, shows the comparison of eight Bergen marine samples based on their functional content using Goodall’s index. Finally it is also possible to compare pathways present in multiple microbial communities using MEGAN’s KEGGviewer. One can compare multiple datasets using different colors see Figure 4.


Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.

Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH - BMC Bioinformatics (2011)

SEED-based functional comparison. Part of a SEED-based functional comparison of eight marine samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3044276&req=5

Figure 2: SEED-based functional comparison. Part of a SEED-based functional comparison of eight marine samples.
Mentions: MEGAN supports the simultaneous analysis and comparison of the taxonomic content and now also the functional content of multiple datasets in several ways. The functional content of a set of metagenomes can be simulteniously opened and compared using a new SEED-based tree view (see Figure 2). Furthermore a collection of datasets can be compared using six different ecological indices, the UniFrac measure [2] and different distance analysis techniques (see [14] for details). As an example Figure 3, shows the comparison of eight Bergen marine samples based on their functional content using Goodall’s index. Finally it is also possible to compare pathways present in multiple microbial communities using MEGAN’s KEGGviewer. One can compare multiple datasets using different colors see Figure 4.

Bottom Line: We have compared our results with the MG-RAST service for different datasets.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076 Tübingen, Germany. mitra@informatik.uni-tuebingen.de.

ABSTRACT

Background: Metagenomics 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.

Results: The 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.

Conclusions: The 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.

Show MeSH