A new method to cluster DNA sequences using Fourier power spectrum.
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.
Department of Mathematics, Statistics and Computer Science, University of Ilinois at Chicago, Chicago, IL 60607, USA.
Tung
T
Hoang
Department of Mathematics, Statistics and Computer Science, University of Ilinois at Chicago, Chicago, IL 60607, USA.
Changchuan
C
Yin
Department of Mathematics, Statistics and Computer Science, University of Ilinois at Chicago, Chicago, IL 60607, USA.
Hui
H
Zheng
Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Flinders University, Adelaide, SA 5001, Australia.
Chenglong
C
Yu
Department of Biological Sciences, Chicago State University, Chicago, IL, USA.
Rong
R
Lucy He
Department of Mathematical Sciences, Tsinghua University, Beijing 100084, China. Electronic address: yau@uic.edu.
Stephen S-T
SS
Yau
D000465:Algorithms; D000818:Animals; D001419:Bacteria / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology; D017934:Coronavirus / Q000235:genetics; D004247:DNA / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005583:Fourier Analysis; D016678:Genome; D016680:Genome, Bacterial; D006801:Humans; D007091:Image Processing, Computer-Assisted; D009980:Influenza A virus / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D012229:Rhinovirus / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
D004272:DNA, Mitochondrial; D004247:DNA
Genes; Moments; Phylogenetic trees