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Open Access Highly Accessed Methodology article

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

Manuel Stark12, Simon A Berger3, Alexandros Stamatakis3 and Christian von Mering1*

Author Affiliations

1 Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland

2 Ph.D. program in Molecular Life Sciences, University of Zurich and Federal Institute of Technology (ETH), Zurich, Switzerland

3 The Exelixis Lab, Department of Computer Science, Technische Universität München, Germany

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BMC Genomics 2010, 11:461  doi:10.1186/1471-2164-11-461

Published: 5 August 2010

Abstract

Background

Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem.

Results

Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/ webcite) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information.

Conclusions

We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.