Integrative analysis of environmental sequences using MEGAN4

  1. Stephan C. Schuster2
  1. 1Center for Bioinformatics, Tübingen University, 72076 Tübingen, Germany;
  2. 2Center for Comparative Genomics, Penn State University, University Park, Pennsylvania 16802, USA

    Abstract

    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.

    Footnotes

    • 3 Corresponding author.

      E-mail huson{at}informatik.uni-tuebingen.de.

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.120618.111. Freely available online through the Genome Research Open Access option.

    • Received January 9, 2011.
    • Accepted June 7, 2011.

    Freely available online through the Genome Research Open Access option.

    | Table of Contents
    OPEN ACCESS ARTICLE

    Preprint Server