AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization

Langenkämper D, Goesmann A, Nattkemper TW (2014)
BMC Bioinformatics 15: 384.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Background: With the advent of low cost, fast sequencing technologies metagenomic analyses are made possible. The large data volumes gathered by these techniques and the unpredictable diversity captured in them are still, however, a challenge for computational biology. Results: In this paper we address the problem of rapid taxonomic assignment with small and adaptive data models (< 5 MB) and present the accelerated k-mer explorer (AKE). Acceleration in AKE's taxonomic assignments is achieved by a special machine learning architecture, which is well suited to model data collections that are intrinsically hierarchical. We report classification accuracy reasonably well for ranks down to order, observed on a study on real world data (Acid Mine Drainage, Cow Rumen). Conclusion: We show that the execution time of this approach is orders of magnitude shorter than competitive approaches and that accuracy is comparable. The tool is presented to the public as a web application.
Stichworte
machine learning; classification; genomics; metagenomics; big data; H2SOM; high performance computing; web-based; acceleration; bioinformatics
Erscheinungsjahr
2014
Zeitschriftentitel
BMC Bioinformatics
Band
15
Art.-Nr.
384
eISSN
1471-2105
Finanzierungs-Informationen
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
Page URI
https://pub.uni-bielefeld.de/record/2705712

Zitieren

Langenkämper D, Goesmann A, Nattkemper TW. AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization. BMC Bioinformatics. 2014;15: 384.
Langenkämper, D., Goesmann, A., & Nattkemper, T. W. (2014). AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization. BMC Bioinformatics, 15, 384. doi:10.1186/s12859-014-0384-0
Langenkämper, D., Goesmann, A., and Nattkemper, T. W. (2014). AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization. BMC Bioinformatics 15:384.
Langenkämper, D., Goesmann, A., & Nattkemper, T.W., 2014. AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization. BMC Bioinformatics, 15: 384.
D. Langenkämper, A. Goesmann, and T.W. Nattkemper, “AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization”, BMC Bioinformatics, vol. 15, 2014, : 384.
Langenkämper, D., Goesmann, A., Nattkemper, T.W.: AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization. BMC Bioinformatics. 15, : 384 (2014).
Langenkämper, Daniel, Goesmann, Alexander, and Nattkemper, Tim Wilhelm. “AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization”. BMC Bioinformatics 15 (2014): 384.
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