MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets

Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A (2013)
Journal of Biotechnology 167(2): 156-165.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Zakrzewski, MarthaUniBi; Bekel, ThomasUniBi; Ander, ChristinaUniBi; Pühler, AlfredUniBi ; Rupp, OliverUniBi; Stoye, JensUniBi ; Schlüter, AndreasUniBi ; Goesmann, AlexanderUniBi
Einrichtung
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Arbeitsgruppe E. Flaschel
Technische Fakultät > AG Fermentationstechnik
Abstract / Bemerkung
Metagenomics aims at exploring microbial communities concerning their composition and functioning. Application of high-throughput sequencing technologies for the analysis of environmental DNA-preparations can generate large sets of metagenome sequence data which have to be analyzed by means of bioinformatics tools to unveil the taxonomic composition of the analyzed community as well as the repertoire of genes and gene functions. A bioinformatics software platform is required that allows the automated taxonomic and functional analysis and interpretation of metagenome datasets without manual effort. To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically accomplishes the tasks necessary for analyzing the composition and functional repertoire of a given microbial community from metagenome sequence data by implementing two software pipelines: (i) the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) the second functional pipeline accomplishes region predictions on assembled contigs and assigns functional information to predicted coding sequences. Moreover, MetaSAMS provides tools for statistical and comparative analyses based on the taxonomic and functional annotations. The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community of a production-scale biogas plant. The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de.
Erscheinungsjahr
2013
Zeitschriftentitel
Journal of Biotechnology
Band
167
Ausgabe
2
Seite(n)
156-165
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/2529202

Zitieren

Zakrzewski M, Bekel T, Ander C, et al. MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology. 2013;167(2):156-165.
Zakrzewski, M., Bekel, T., Ander, C., Pühler, A., Rupp, O., Stoye, J., Schlüter, A., et al. (2013). MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology, 167(2), 156-165. doi:10.1016/j.jbiotec.2012.09.013
Zakrzewski, Martha, Bekel, Thomas, Ander, Christina, Pühler, Alfred, Rupp, Oliver, Stoye, Jens, Schlüter, Andreas, and Goesmann, Alexander. 2013. “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”. Journal of Biotechnology 167 (2): 156-165.
Zakrzewski, M., Bekel, T., Ander, C., Pühler, A., Rupp, O., Stoye, J., Schlüter, A., and Goesmann, A. (2013). MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology 167, 156-165.
Zakrzewski, M., et al., 2013. MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology, 167(2), p 156-165.
M. Zakrzewski, et al., “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”, Journal of Biotechnology, vol. 167, 2013, pp. 156-165.
Zakrzewski, M., Bekel, T., Ander, C., Pühler, A., Rupp, O., Stoye, J., Schlüter, A., Goesmann, A.: MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology. 167, 156-165 (2013).
Zakrzewski, Martha, Bekel, Thomas, Ander, Christina, Pühler, Alfred, Rupp, Oliver, Stoye, Jens, Schlüter, Andreas, and Goesmann, Alexander. “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”. Journal of Biotechnology 167.2 (2013): 156-165.

9 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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