title: 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.
authors.affiliation: School of Mathematical Sciences, Dalian University of Technology, Dalian 116024, PR China.
authors.forename: Wenbing
authors.initials: W
authors.lastname: Hou
authors.affiliation: School of Innovation and Entrepreneurship, Dalian University of Technology, Dalian 116024, PR China; School of Mathematical Sciences, Dalian University of Technology, Dalian 116024, PR China.
authors.forename: Qiuhui
authors.initials: Q
authors.lastname: Pan
authors.affiliation: Department of Academics, Dalian Naval Academy, Dalian 116001, PR China.
authors.forename: Qianying
authors.initials: Q
authors.lastname: Peng
authors.affiliation: School of Mathematical Sciences, Dalian University of Technology, Dalian 116024, PR China. Electronic address: mfhe@dlut.edu.cn.
authors.forename: Mingfeng
authors.initials: M
authors.lastname: He
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D006801:Humans; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins
keywords: Discrete Fourier Transform; Dynamic Time Warping; Phylogenetic tree; Protein sequences similarity analysis