Classification of genomic signals using dynamic time warping

BMC Bioinformatics

Research

Helena Skutkova¹  Martin Vitek²  Ivo Provaznik²  Rene Kizek³  Petr Babula⁴ 

[1] Department of Biomedical Engineering, Brno University of Technology, Technicka 12, CZ -616 00, Brno, Czech Republic;Department of Biomedical Engineering, Brno University of Technology, Technicka 12, CZ -616 00, Brno, Czech Republic;International Clinical Research Center - Center of Biomedical Engineering, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic;Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ - 613 00, Brno, Czech Republic;International Clinical Research Center - Center of Biomedical Engineering, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic;

关键词: Dynamic Time Warping;    Biological Sequence;    Symbolic Sequence;    Genomic Signal;    Distance Difference;   

DOI  :  10.1186/1471-2105-14-S10-S1

来源: Springer

【 摘 要 】

BackgroundClassification methods of DNA most commonly use comparison of the differences in DNA symbolic records, which requires the global multiple sequence alignment. This solution is often inappropriate, causing a number of imprecisions and requires additional user intervention for exact alignment of the similar segments. The similar segments in DNA represented as a signal are characterized by a similar shape of the curve. The DNA alignment in genomic signals may adjust whole sections not only individual symbols. The dynamic time warping (DTW) is suitable for this purpose and can replace the multiple alignment of symbolic sequences in applications, such as phylogenetic analysis.MethodsThe proposed method is composed of three main parts. The first part represent conversion of symbolic representation of DNA sequences in the form of a string of A,C,G,T symbols to signal representation in the form of cumulated phase of complex components defined for each symbol. Next part represents signals size adjustment realized by standard signal preprocessing methods: median filtration, detrendization and resampling. The final part necessary for genomic signals comparison is position and length alignment of genomic signals by dynamic time warping (DTW).ResultsThe application of the DTW on set of genomic signals was evaluated in dendrogram construction using cluster analysis. The resulting tree was compared with a classical phylogenetic tree reconstructed using multiple alignment. The classification of genomic signals using the DTW is evolutionary closer to phylogeny of organisms. This method is more resistant to errors in the sequences and less dependent on the number of input sequences.ConclusionsClassification of genomic signals using dynamic time warping is an adequate variant to phylogenetic analysis using the symbolic DNA sequences alignment; in addition, it is robust, quick and more precise technique.

【 授权许可】

Unknown   
© Skutkova et al; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.