A new method to cluster DNA sequences using Fourier power spectrum

Journal of Theoretical Biology
Tung HoangStephen S-T Yau

Abstract

A novel clustering method is proposed to classify genes and genomes. For a given DNA sequence, a binary indicator sequence of each nucleotide is constructed, and Discrete Fourier Transform is applied on these four sequences to attain respective power spectra. Mathematical moments are built from these spectra, and multidimensional vectors of real numbers are constructed from these moments. Cluster analysis is then performed in order to determine the evolutionary relationship between DNA sequences. The novelty of this method is that sequences with different lengths can be compared easily via the use of power spectra and moments. Experimental results on various datasets show that the proposed method provides an efficient tool to classify genes and genomes. It not only gives comparable results but also is remarkably faster than other multiple sequence alignment and alignment-free methods.

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Citations

Feb 2, 2016·Journal of Theoretical Biology·Lianping YangChenhui Yang
Aug 25, 2015·Journal of Theoretical Biology·Helena SkutkovaIvo Provaznik
Nov 4, 2015·BMC Bioinformatics·Saulo Alves AflitosDick de Ridder
Dec 23, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hsin-Hsiung Huang, Senthil B Girimurugan
Jul 1, 2018·Statistical Applications in Genetics and Molecular Biology·Hsin-Hsiung HuangJie Yang
Aug 15, 2019·PloS One·Tyler J Dougan, Stephen R Quake
May 12, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nan SunStephen S-T Yau
Mar 8, 2019·Scientific Reports·Ajay Kumar SawSoumyadeep Nandi
Jun 19, 2019·Evolutionary Bioinformatics Online·Tomáš FarkašMária Lucká
Dec 31, 2019·BioMed Research International·Mervat M Abo-ElkhierMoheb I Abo El Maaty
Mar 5, 2016·Journal of Mathematical Biology·Changchuan Yin, Jiasong Wang
Sep 16, 2018·Scientific Reports·Lina ZhangChengjin Zhang
Jan 31, 2018·PeerJ·Gerardo Mendizabal-RuizJ Alejandro Morales
Apr 27, 2019·Frontiers in Genetics·Rui DongStephen S-T Yau
Feb 18, 2019·Statistical Applications in Genetics and Molecular Biology·Hsin-Hsiung Huang, Senthil Balaji Girimurugan
Jul 3, 2021·Genes·Enrique Canessa

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Software Mentioned

MAFFT
ClustalW
MATLAB
MEGA

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