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.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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.
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Zeitschriftentitel
BMC Bioinformatics
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15
Artikelnummer
384
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Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
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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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2 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.
Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG., BMC Bioinformatics 17(), 2016
PMID: 26774270
Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.
Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW., Front Genet 7(), 2016
PMID: 26904094

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