Original title: Alignment-free Methods for Classification of Metagenomic Data
Authors: Vaněčková, Tereza
Document type: Papers
Language: eng
Publisher: Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií
Abstract: Metagenomics studies microbial communities by analyzing their genomic content directly sequenced from the environment. In this contribution, alignment-free methods based on word frequency will be introduced. It has been proven, that these methods are effective in processing of short metagenomic sequence reads produced by Next-Generation Sequencing technologies. To evaluate the potential of word frequency based methods, the k-mer analysis was applied on simulated dataset of metagenomic sequence reads with length of 600 nucleotides. Then the data were enrolled for a hierarchical cluster analysis. Results have shown that the proposed method is able to cluster genome fragments of the same taxa.
Keywords: alignment-free; hierarchical clustering; metagenomics; nucleotide word frequency
Host item entry: Proceedings of the 22nd Conference STUDENT EEICT 2016, ISBN 978-80-214-5350-0

Institution: Brno University of Technology (web)
Document availability information: Fulltext is available in the Brno University of Technology Digital Library.
Original record: http://hdl.handle.net/11012/83930

Permalink: http://www.nusl.cz/ntk/nusl-383648


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