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Taxonomic metagenome sequence assignment with structured output models

Nature Methods volume 8, pages 191–192 (2011)Cite this article

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To the Editor:

Computational inference of the taxonomic origin of sequence fragments is an essential step in metagenome analysis1. Fragments can be assigned to individual populations or corresponding higher-level evolutionary clades using methods based on homology, sequence similarity or sequence composition2. This is a challenging task, as for most uncultured microorganisms reference sequences are unavailable, and large amounts of data have to be processed. With this in mind, we introduce PhyloPythiaS a successor of our previously published method PhyloPythia3. It is a fast and accurate sequence compositional classifier based on the structured output paradigm4.

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Figure 1: Comparison of taxonomic classification methods.

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Acknowledgements

We thank T. Joachims for the SVMstruct implementation, L. Steinbrück and L. Feuerbach for software testing. K.R.P. and A.C.M. were funded by the Max Planck society and Heinrich Heine University Düsseldorf. T.S. acknowledges support from the German Science Foundation (Deutsche Forschungsgemeinschaft. P.J.T. is funded by US National Institutes of Health (P50 GM068763). The unpublished data for the WG-1 project was collected with support provided by the Office of the Chief Executive (OCE) Science team of Commonwealth Scientific and Industrial Research Organization Australia, in the form of an OCE postdoctoral fellowship (P.B.P.) and OCE Science Leader program (M.M.).

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Authors and Affiliations

  1. Max-Planck Research Group for Computational Genomics and Epidemiology, Max Planck Institute for Informatics, Saarbrücken, Germany

    Kaustubh R Patil & Alice C McHardy

  2. Department of Computer Science, University of Potsdam, Potsdam, Germany

    Peter Haider & Tobias Scheffer

  3. Commonwealth Scientific and Industrial Research Organization Livestock Industries, Queensland Bioscience Precinct, St Lucia, Australia

    Phillip B Pope & Mark Morrison

  4. Harvard Faculty of Arts and Sciences Center for Systems Biology, Cambridge, Massacusetts, USA

    Peter J Turnbaugh

  5. Department of Algorithmic Bioinformatics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany

    Alice C McHardy

Authors
  1. Kaustubh R Patil
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  2. Peter Haider
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  3. Phillip B Pope
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  4. Peter J Turnbaugh
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  5. Mark Morrison
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  6. Tobias Scheffer
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  7. Alice C McHardy
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Correspondence to Alice C McHardy.

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Supplementary Figures 1–5, Supplementary Tables 1–14, Supplementary Note (PDF 1998 kb)

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Patil, K., Haider, P., Pope, P. et al. Taxonomic metagenome sequence assignment with structured output models. Nat Methods 8, 191–192 (2011). https://doi.org/10.1038/nmeth0311-191

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