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Classification of genomic signals using dynamic time warping.

Skutkova H, Vitek M, Babula P, Kizek R, Provaznik I - BMC Bioinformatics (2013)

Bottom Line: 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.Classification 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.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Classification 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.

Methods: The 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).

Results: The 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.

Conclusions: Classification 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.

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Genomic signals after DTW. Upper - the alignment of human and rhesus macaque genomic signals; lower - the alignment of human and chicken genomic signals.
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Figure 2: Genomic signals after DTW. Upper - the alignment of human and rhesus macaque genomic signals; lower - the alignment of human and chicken genomic signals.

Mentions: The application of the DTW on genomic signals is shown in Figure 2. It is no surprise that the signals of ACTA1 from rhesus macaque and human are not very different. The use of the DTW in the case of alignment of human and chicken ACTA1 was more necessary. The resulting signals in Figure 2 (lower image) are significantly positionally adapted. The difference between aligned signals is caused by an insufficient amplitude adjustment.


Classification of genomic signals using dynamic time warping.

Skutkova H, Vitek M, Babula P, Kizek R, Provaznik I - BMC Bioinformatics (2013)

Genomic signals after DTW. Upper - the alignment of human and rhesus macaque genomic signals; lower - the alignment of human and chicken genomic signals.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750471&req=5

Figure 2: Genomic signals after DTW. Upper - the alignment of human and rhesus macaque genomic signals; lower - the alignment of human and chicken genomic signals.
Mentions: The application of the DTW on genomic signals is shown in Figure 2. It is no surprise that the signals of ACTA1 from rhesus macaque and human are not very different. The use of the DTW in the case of alignment of human and chicken ACTA1 was more necessary. The resulting signals in Figure 2 (lower image) are significantly positionally adapted. The difference between aligned signals is caused by an insufficient amplitude adjustment.

Bottom Line: 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.Classification 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.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Classification 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.

Methods: The 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).

Results: The 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.

Conclusions: Classification 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.

Show MeSH