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. 2013 Apr 15;29(8):973-80.
doi: 10.1093/bioinformatics/btt077. Epub 2013 Feb 15.

V体育ios版 - Protein signature-based estimation of metagenomic abundances including all domains of life and viruses

Heiner Klingenberg  1 , Kathrin Petra Aßhauer, Thomas Lingner, Peter Meinicke
Affiliations

Protein signature-based estimation of metagenomic abundances including all domains of life and viruses

Heiner Klingenberg et al. Bioinformatics. .

Abstract

Motivation: Metagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling VSports手机版. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases. .

Results: We introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures V体育安卓版. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure. .

Availability: http://gobics. de/TaxyPro V体育ios版. .

Supplementary information: Supplementary Material is available at Bioinformatics online VSports最新版本. .

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Figures

Fig. 1.
Fig. 1.
Estimated fraction of archaeal and bacterial DNA for the Oil Seep dataset using different tools
Fig. 2.
Fig. 2.
Accuracy of different profiling methods on test datasets from two archaeal genomes using simulated 450 bp reads (see text)
Fig. 3.
Fig. 3.
Estimated fraction of viral DNA in the Freshwater (top) and Rumen (bottom) metagenomes using different profiling tools (see text)
Fig. 4.
Fig. 4.
FDU/FSU scatter plot based on 1494 HMP datasets. See text for explanation of markers
See this image and copyright information in PMC

References

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