Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Taxonomic metagenome sequence assignment with structured output models

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

Subjects

To the Editor:

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Comparison of taxonomic classification methods.

References

  1. Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. & Hugenholtz, P. Microbiol. Mol. Biol. Rev. 72, 557–578 (2008).

    Article  CAS  Google Scholar 

  2. McHardy, A.C. & Rigoutsos, I. Curr. Opin. Microbiol. 10, 499–503 (2007).

    Article  CAS  Google Scholar 

  3. McHardy, A.C., Garcia-Martin, H., Tsirigos, A., Hugenholtz, P. & Rigoutsos, I. Nat. Methods 4, 63–72 (2007).

    Article  CAS  Google Scholar 

  4. Tsochantaridis, I., Joachims, T., Hofmann, T. & Altun, Y. J. Mach. Learn. Res. 6, 1453-1484 (2005).

  5. Huson, D.H., Auch, A.F., Qi, J. & Schuster, S.C. Genome Res. 17, 377–386 (2007).

    Article  CAS  Google Scholar 

  6. Brady, A. & Salzberg, S.L. Nat. Methods 6, 673–676 (2009).

    Article  CAS  Google Scholar 

Download references

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 The unpublished data for the WG-1 project was collected with support provided by the Office of the Chief Executive (OCE) Science team of Commonwealth Scientific and Industrial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.).

Author information

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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peter Haider
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Phillip B Pope
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Peter J Turnbaugh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mark Morrison
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Tobias Scheffer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alice C McHardy
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alice C McHardy.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

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

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth0311-191

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing