A new method to cluster genomes based on cumulative Fourier power spectrum

Rui Dong Tsinghua University Ziyue Zhu Tsinghua University Changchuan Yin University of Illinois at Chicago Rong L. He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1903.42005

Gene, 673, 2018.6
Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum).
Cumulative Fourier power spectrum, Moment vectors, DNA sequences, Phylogenetic trees
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@inproceedings{rui2018a,
  title={A new method to cluster genomes based on cumulative Fourier power spectrum},
  author={Rui Dong, Ziyue Zhu, Changchuan Yin, Rong L. He, and Stephen S.-T. Yau},
  url={http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20190318103215356355203},
  booktitle={Gene},
  volume={673},
  year={2018},
}
Rui Dong, Ziyue Zhu, Changchuan Yin, Rong L. He, and Stephen S.-T. Yau. A new method to cluster genomes based on cumulative Fourier power spectrum. 2018. Vol. 673. In Gene. http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20190318103215356355203.
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