Phylogenetic classification of short environmental DNA fragments

Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J (2008)
Nucleic Acids Research 36(7): 2230-2239.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.
Erscheinungsjahr
2008
Zeitschriftentitel
Nucleic Acids Research
Band
36
Ausgabe
7
Seite(n)
2230-2239
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/1783364

Zitieren

Krause L, Diaz NN, Goesmann A, et al. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research. 2008;36(7):2230-2239.
Krause, L., Diaz, N. N., Goesmann, A., Kelley, S., Nattkemper, T. W., Rohwer, F., Edwards, R. A., et al. (2008). Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36(7), 2230-2239. doi:10.1093/nar/gkn038
Krause, L., Diaz, N. N., Goesmann, A., Kelley, S., Nattkemper, T. W., Rohwer, F., Edwards, R. A., and Stoye, J. (2008). Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research 36, 2230-2239.
Krause, L., et al., 2008. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36(7), p 2230-2239.
L. Krause, et al., “Phylogenetic classification of short environmental DNA fragments”, Nucleic Acids Research, vol. 36, 2008, pp. 2230-2239.
Krause, L., Diaz, N.N., Goesmann, A., Kelley, S., Nattkemper, T.W., Rohwer, F., Edwards, R.A., Stoye, J.: Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research. 36, 2230-2239 (2008).
Krause, Lutz, Diaz, Naryttza N., Goesmann, Alexander, Kelley, Scott, Nattkemper, Tim Wilhelm, Rohwer, Forest, Edwards, Robert A., and Stoye, Jens. “Phylogenetic classification of short environmental DNA fragments”. Nucleic Acids Research 36.7 (2008): 2230-2239.
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2019-09-06T08:48:51Z
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