Dataset Information

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

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.

SUBMITTER: Pei S

PROVIDER: S-EPMC6661692 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Pei Shaojun S Dong Rui R He Rong Lucy RL Yau Stephen S-T SS

Computational and structural biotechnology journal 20190711

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 spec ...[more]

PMID: 31384399

Similar Datasets

Project description:To investigate the correlation and stationarity of noise in volumetric computed tomography (CT) using the local discrete noise-power spectrum (NPS) and off-diagonal elements of the covariance matrix of the discrete Fourier transform of noise-only images (denoted Σ(DFT)). Experimental conditions were varied to affect noise correlation and stationarity, the effects were quantified in terms of the NPS and Σ(DFT), and practical considerations in CT performance characterization were identified.Cone-beam CT (CBCT) images were acquired using a benchtop system comprising an x-ray tube and flat-panel detector for a range of acquisition techniques (e.g., dose and x-ray scatter) and three phantom configurations hypothesized to impart distinct effects on the NPS and Σ(DFT): (A) air, (B) a 20-cm-diameter water cylinder with a bowtie filter, and (C) the cylinder without a bowtie filter. The NPS and off-diagonal elements of the Σ(DFT) were analyzed as a function of position within the reconstructions.The local NPS varied systematically throughout the axial plane in a manner consistent with changes in fluence transmitted to the detector and view sampling effects. Variability in fluence was manifest in the NPS magnitude-e.g., a factor of ~2 variation in NPS magnitude within the axial plane for case C (cylinder without bowtie), compared to nearly constant NPS magnitude for case B (bowtie filter matched to the cylinder). View sampling effects were most prominent in case A (air) where the variance increased at greater distance from the center of reconstruction and in case C (cylinder) where the NPS exhibited correlations in the radial direction. The effects of detector lag were observed as azimuthal correlation. The cylinder (without bowtie) had the strongest nonstationarity because of the larger variability in fluence transmitted to the detector. The diagonal elements of the Σ(DFT) were equivalent to the NPS estimated from the periodogram, and the average off-diagonal elements of the Σ(DFT) exhibited amplitude of ~1% of the NPS for the experimental conditions investigated. Furthermore, the off-diagonal elements demonstrated fairly long tails of nearly constant amplitude, with magnitude somewhat reduced for experimental conditions associated with greater stationarity (viz., lower Σ(DFT) tails for cases A and B in comparison to case C).Volumetric CT exhibits nonstationarity in the NPS as hypothesized in relation to fluence uniformity and view sampling. Measurement of the NPS should seek to minimize such changes in noise correlations and include careful reporting of experimental conditions (e.g., phantom design and use of a bowtie filter) and spatial dependence (e.g., analysis at fixed radius within a phantom). Off-diagonal elements of the Σ(DFT) similarly depend on experimental conditions and can be readily computed from the same data as the NPS. This work begins to check assumptions in NPS analysis examine the extent to which NPS is an appropriate descriptor of noise correlations, and investigate the magnitude of off-diagonal elements of the Σ(DFT). While the magnitude of such off-diagonal elements appears to be low, their cumulative effect on space-variant detectability remains to be investigated-e.g., using task-specific figures of merit.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets