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Bioinformatics Advance Access originally published online on June 10, 2009
Bioinformatics 2009 25(15):1849-1855; doi:10.1093/bioinformatics/btp341
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Visual and statistical comparison of metagenomes

Suparna Mitra 1,*, Bernhard Klar 2 and Daniel H. Huson 1

1 Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076 Tübingen and 2 Institute for Stochastics, Karlsruhe University, Kaiserstraße 89, 76133 Karlsruhe, Germany

* To whom correspondence should be addressed.


  Abstract

Background: Metagenomics is the study of the genomic content of an environmental sample of microbes. Advances in the through-put and cost-efficiency of sequencing technology is fueling a rapid increase in the number and size of metagenomic datasets being generated. Bioinformatics is faced with the problem of how to handle and analyze these datasets in an efficient and useful way. One goal of these metagenomic studies is to get a basic understanding of the microbial world both surrounding us and within us. One major challenge is how to compare multiple datasets. Furthermore, there is a need for bioinformatics tools that can process many large datasets and are easy to use.

Results: This article describes two new and helpful techniques for comparing multiple metagenomic datasets. The first is a visualization technique for multiple datasets and the second is a new statistical method for highlighting the differences in a pairwise comparison. We have developed implementations of both methods that are suitable for very large datasets and provide these in Version 3 of our standalone metagenome analysis tool MEGAN.

Conclusion: These new methods are suitable for the visual comparison of many large metagenomes and the statistical comparison of two metagenomes at a time. Nevertheless, more work needs to be done to support the comparative analysis of multiple metagenome datasets.

Availability: Version 3 of MEGAN, which implements all ideas presented in this article, can be obtained from our web site at: www-ab.informatik.uni-tuebingen.de/software/megan.

Contact: mitra{at}informatik.uni-tuebingen.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on January 26, 2009; revised on May 29, 2009; accepted on May 29, 2009

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