Large-Scale Genome Comparison Based on Cumulative Fourier Power and Phase Spectra: Central Moment and Covariance Vector

Computational and Structural Biotechnology Journal
Shaojun PeiStephen S-T Yau

Abstract

Genome comparison is a vital research area of bioinformatics. For large-scale genome comparisons, the Multiple Sequence Alignment (MSA) methods have been impractical to use due to its algorithmic complexity. In this study, we propose a novel alignment-free method based on the one-to-one correspondence between a DNA sequence and its complete central moment vector of the cumulative Fourier power and phase spectra. In addition, the covariance between the four nucleotides in the power and phase spectra is included. We use the cumulative Fourier power and phase spectra to define a 28-dimensional vector for each DNA sequence. Euclidean distances between the vectors can measure the dissimilarity between DNA sequences. We perform testing with datasets of different sizes and types including simulated DNA sequences, exon-intron and complete genomes. The results show that our method is more accurate and efficient for performing hierarchical clustering than other alignment-free methods and MSA methods.

Citations

May 12, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nan SunStephen S-T Yau
Aug 11, 2020·Computational and Structural Biotechnology Journal·Zeju SunStephen S-T Yau
Oct 31, 2020·Medical & Biological Engineering & Computing·Mingyang LiWanzhong Chen

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Software Mentioned

UPGMA
MAFFT
MATLAB
CentOS 7 Linux Server
Linux
MSAProbs
Clustal Omega
Mega7
MEGA

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