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

Bioinformatics

Volumn 29, Issue 8, 2013, Pages 973-980

  Klingenberg, Heiner ^a   Aßhauer, Kathrin Petra ^a   Lingner, Thomas ^a   Meinicke, Peter ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA;

ARCHAEAL DNA; VIRUS DNA;

ARTICLE; HUMAN; METAGENOME; METAGENOMICS; METHODOLOGY; PHYLOGENY; PROTEIN TERTIARY STRUCTURE;

DNA, ARCHAEAL; DNA, VIRAL; HUMANS; METAGENOME; METAGENOMICS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY;

EID: 84876263402     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt077     Document Type: Article

References (31)

1. Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Berg Miller, M.E. et al. (2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ. Microbiol., 14, 207-227.
3. Brady, A. and Salzberg, S. (2011) PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat. Methods, 8, 367.
4. Brady, A. and Salzberg, S.L. (2009) Phymm and PhymmBL: metagenomicphylogen- etic classification with interpolated Markov models. Nat. Methods, 6, 673-676.
5. Bray, J.R. and Curtis, J.T. (1957) An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr., 27, 325-349.
6. Dempster, A.P. et al. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. Series B Stat. Methodol., 39, 1-22.
7. Diaz, N.N. et al. (2009) TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10, 56.
8. Duhaime, M.B. et al. (2012) Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and opti- mization of the linker amplification method. Environ. Microbiol., 14, 2526-2537.
9. Finn, R.D. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
10. Finn, R.D. et al. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
11. Havelsrud, O.E. et al. (2011) A metagenomic study ofmethanotrophic microorgan- isms in Coal Oil Point seep sediments. BMC Microbiol., 11, 221.
12. Huson, D.H. et al. (2007) MEGAN analysis ofmetagenomic data. Genome Res., 17, 377-386.
13. Huttenhower, C. et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
14. Krause, L. et al. (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res., 36, 2230-2239.
15. Lingner, T. et al. (2010) Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMCBioinformatics, 11, 481.
16. Lingner, T. et al. (2011) CoMet-a web server for comparative functional profiling of metagenomes. Nucleic Acids Res., 39, W518-W523.
17. Liu, B. et al. (2011) Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics, 12 (Suppl. 2), S4.
18. Meinicke, P. et al. (2011) Mixture models for analysis of the taxonomic composition ofmetagenomes. Bioinformatics, 27, 1618-1624.
19. Meyer, F. et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 386.
20. Mokili, J.L. et al. (2012) Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol., 2, 63-77.
21. Monzoorul Haque, M. et al. (2009) SOrt-ITEMS: sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics, 25, 1722-1730.
22. Parks, D.H. et al. (2011) Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics, 12, 328.
23. Peterson, J. et al. (2009) The NIH human microbiome project. Genome Res., 19, 2317-2323.
24. Rho, M. et al. (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res., 38, e191.
25. Richter, D.C. et al. (2008) MetaSim: a sequencing simulator for genomics and meta- genomics. PLoS ONE, 3, e3373.
26. Rosen, G.L. and Lim, T.Y. (2012) NBC update: the addition of viral and fungal databases to the Naïve Bayes classification tool. BMC Res. Notes, 5, 81.
27. Rosen, G.L. et al. (2011) NBC: the Naïve Bayes Classification tool webserver for taxonomic classification ofmetagenomic reads. Bioinformatics, 27, 127-129.
28. Schreiber, F. et al. (2010) Treephyler: fast taxonomic profiling of metagenomes. Bioinformatics, 26, 960-961.
29. Segata, N. et al. (2012a) Composition of the adult digestive tract bacterial micro- biome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol., 13, R42.
30. Segata, N. et al. (2012b) Metagenomic microbial community profiling using unique clade-specificmarkergenes. Nat. Methods, 9, 811-814.
31. Xu, J. et al. (2007) Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proc. Natl Acad. Sci. U S A, 104, 18730-18735.