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Register a new userA Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform
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Added by
Changchuan Yin Dr.
Publication date
2014
fields
Informatics Engineering
and research's language is
English
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Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on high level of sequence identity, however, most of the existing alignment-free methods do not employ true full information content of sequences and thus can not accurately reveal similarities and differences among DNA sequences. We present a novel alignment-free computational method for sequence analysis based on Ramanujan-Fourier transform (RFT), in which complete information of DNA sequences is retained. We represent DNA sequences as four binary indicator sequences and apply RFT on the indicator sequences to convert them into frequency domain. The Euclidean distance of the complete RFT coefficients of DNA sequences are used as similarity measure. To address the different lengths in Euclidean space of RFT coefficients, we pad zeros to short DNA binary sequences so that the binary sequences equal the longest length in the comparison sequence data. Thus, the DNA sequences are compared in the same dimensional frequency space without information loss. We demonstrate the usefulness of the proposed method by presenting experimental results on hierarchical clustering of genes and genomes. The proposed method opens a new channel to biological sequence analysis, classification, and structural module identification.
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DNA sequences are fundamental for encoding genetic information. The genetic information may not only be understood by symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed into numerical sequences so the hidden signals can be revealed by signal processing techniques. All current transformation methods encode DNA sequences into numerical values of the same length. These representations have limitations in the applications of genomic signal compression, encryption, and steganography. We propose an integer chaos game representation (iCGR) of DNA sequences and a lossless encoding method DNA sequences by the iCGR. In the iCGR method, a DNA sequence is represented by the iterated function of the nucleotides and their positions in the sequence. Then the DNA sequence can be uniquely encoded and recovered using three integers from iCGR. One integer is the sequence length and the other two integers represent the accumulated distributions of nucleotides in the sequence. The integer encoding scheme can compress a DNA sequence by 2 bits per nucleotide. The integer representation of DNA sequences provides a prospective tool for sequence compression, encryption, and steganography. The Python programs in this study are freely available to the public at https://github.com/cyinbox/iCGR
We demonstrate a fast numerical method of theoretical studies of skyrmion lattice or spiral order in magnetic materials with Dzyaloshinsky-Moriya interaction. The method is based on the Fourier expansion of the magnetization combined with a minimization of the free energy functional of the magnetic material in Fourier space, yielding the optimal configuration of the system for any given set of parameters. We employ a Lagrange multiplier technique in order to satisfy micromagnetic constraints. We apply this method to a system that exhibits, depending on the parameter choice, ferromagnetic, skyrmion lattice, or spiral (helical) order. Known critical fields corresponding to the helical-skyrmion as well as the skyrmion-ferromagnet phase transitions are reproduced with high precision. Using this numerical method we predict new types of excited (metastable) states of the skyrmion lattice, which may be stabilized by coupling the skyrmion lattice with a superconducting vortex lattice. The method can be readily adapted to other micromagnetic systems.
The focus of this paper is on the analysis of the Conjugate Gradient method applied to a non-symmetric system of linear equations, arising from a Fast Fourier Transform-based homogenization method due to (Moulinec and Suquet, 1994). Convergence of the method is proven by exploiting a certain projection operator reflecting physics of the underlying problem. These results are supported by a numerical example, demonstrating significant improvement of the Conjugate Gradient-based scheme over the original Moulinec-Suquet algorithm.
Limit analysis is a computationally efficient tool to assess the resistance and the failure mode of structures but does not provide any information on the displacement capacity, which is one of the concepts which most affects the seismic safety. Therefore, since many researchers did not consider limit analysis as a possible tool for the seismic assessment of structures, its widespread employment has been prevented. In this paper this common belief is questioned and the authors show that limit analysis can be useful in the evaluation of the seismic performance of frame structures. In particular, to overcome the limitation on the possibility to evaluate the displacements of a structure based on a limit analysis approach, an approximated capacity curve is reconstructed. The latter is based on a limit analysis strategy, which takes into account the second order effects, and evaluates the displacement capacity considering a post-peak softening branch and a threshold on the allowed plastic rotations. Then, based on this simplified capacity curve, an equivalent single degree of freedom system is defined in order to assess the seismic performance of frame structures. The proposed simplified strategy is implemented in a dedicated software and the obtained results are validated with well-established approaches based on nonlinear static analyses, showing the reliability and the computational efficiency of this methodology
This study presents a meshless-based local reanalysis (MLR) method. The purpose of this study is to extend reanalysis methods to the Kriging interpolation meshless method due to its high efficiency. In this study, two reanalysis methods: combined approximations CA) and indirect factorization updating (IFU) methods are utilized. Considering the computational cost of meshless methods, the reanalysis method improves the efficiency of the full meshless method significantly. Compared with finite element method (FEM)-based reanalysis methods, the main superiority of meshless-based reanalysis method is to break the limitation of mesh connection. The meshless-based reanalysis is much easier to obtain the stiffness matrix even for solving the mesh distortion problems. However, compared with the FEM-based reanalysis method, the critical challenge is to use much more nodes in the influence domain due to high order interpolation. Therefore, a local reanalysis method which only needs to calculate the local stiffness matrix in the influence domain is suggested to improve the efficiency further. Several typical numerical examples are tested and the performance of the suggested method is verified.
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