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A new method to analyze protein sequence similarity using Dynamic Time Warping.

ABSTRACT: Sequences similarity analysis is one of the major topics in bioinformatics. It helps researchers to reveal evolution relationships of different species. In this paper, we outline a new method to analyze the similarity of proteins by Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW). The original symbol sequences are converted to numerical sequences according to their physico-chemical properties. We obtain the power spectra of sequences from DFT and extend the spectra to the same length to calculate the distance between different sequences by DTW. Our method is tested in different datasets and the results are compared with that of other software algorithms. In the comparison we find our scheme could amend some wrong classifications appear in other software. The comparison shows our approach is reasonable and effective.

SUBMITTER: Hou W

PROVIDER: S-EPMC7125777 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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A new method to analyze protein sequence similarity using Dynamic Time Warping.

Hou Wenbing W Pan Qiuhui Q Peng Qianying Q He Mingfeng M

Genomics 20161211 2

Sequences similarity analysis is one of the major topics in bioinformatics. It helps researchers to reveal evolution relationships of different species. In this paper, we outline a new method to analyze the similarity of proteins by Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW). The original symbol sequences are converted to numerical sequences according to their physico-chemical properties. We obtain the power spectra of sequences from DFT and extend the spectra to the same le ...[more]

PMID: 27974244

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Project description:Post-stroke complications are the second most frequent cause of death and the third leading cause of disability worldwide. The motor function of post-stroke patients is often assessed by measuring the postural sway in the patients during quiet standing, based on sway measures, such as sway area and velocity, which are obtained from temporal variations of the center of pressure. However, such approaches to establish a relationship between the sway measures and patients' demographic factors have hardly been successful (e.g., days after onset). This study instead evaluates the postural sway features of post-stroke patients using the clustering method of machine learning. First, we collected the stroke patients' multi-variable motion-capture standing-posture data and processed them into t s long data slots. Then, we clustered the t-s data slots into K cluster groups using the dynamic-time-warping partition-around-medoid (DTW-PAM) method. The DTW measures the similarity between two temporal sequences that may vary in speed, whereas PAM identifies the centroids for the DTW clustering method. Finally, we used a post-hoc test and found that the sway amplitudes of markers in the shoulder, hip, knee, and center-of-mass are more important than their sway frequencies. We separately plotted the marker amplitudes and frequencies in the medial-lateral direction during a 5-s data slot and found that the post-stroke patients' postural sway frequency lay within the bandwidth of 0.5-1.5 Hz. Additionally, with an increase in the onset days, the cluster index of cerebral hemorrhage patients gradually transits in a four-cluster solution. However, the cerebral infarction patients did not exhibit such pronounced transitions over time. Moreover, we found that the postural-sway amplitude increased in clusters 1, 3, and 4. However, the amplitude of cluster 2 did not follow this pattern, owing to age effects related to the postural sway changes with age. A rehabilitation doctor can utilize these findings as guidelines to direct the post-stroke patient training.

Dataset Information

A new method to analyze protein sequence similarity using Dynamic Time Warping.

Publications

A new method to analyze protein sequence similarity using Dynamic Time Warping.

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