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In this paper, we propose a new method for gene finding. The method uses a new dynamic representation scheme to map DNA sequences into a numerical form. The dynamic representation scheme assigns numerical pairs to the nucleotides based on their effectiveness in the period-3 spectrum. Nucleotides that have a stronger participation in the period-3 spectrum peaks are assigned numerical pairs that further...
This paper presents a new technique for the detection of short exons in DNA sequences. In this method, we analyze the DNA propeller twist and bending stiffness using the autoregressive (AR) model. The linear prediction matrices for the two features are combined to find the same set of linear prediction coefficients, from which we estimate the spectrum of the DNA sequence and detect protein-coding...
Analysis of DNA sequences requires conversion of a base sequence to a numerical sequence. The choice of the numerical mapping of a DNA sequence affects how well its biological properties can be reflected in the numerical domain for the detection of regions of interest. This paper presents twelve one-sequence numerical representation methods and a discrete Fourier transform (DFT) based approach to...
Tandem repeats, which occur frequently in genomes, are related to gene regulatory functions and various diseases. In this paper, an efficient algorithm for tandem repeat detection is proposed. In our method, the spectrogram of a DNA sequence is analyzed based on the autoregressive model. Then, significant peaks in the spectrogram are selected, and the corresponding regions in the DNA sequence are...
The presence of repeated sequences is a fundamental feature of genomes and detection of repeats is important in biology and medicine as it can be used for phylogenic studies and disease diagnosis. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length. This paper presents results...
The detection of tandem repeats is important in biology and medicine as it can be used for phylogenic studies and disease diagnosis. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length. This paper presents results obtained with a modified product spectrum and BW spectrograms to...
The detection of tandem repeats is important in biology and medicine as it can be used for phylogenic studies and disease diagnosis. This paper presents results obtained with spectral techniques using Fourier analysis for detecting approximate tandem repeats (ATRs) in DNA sequences. These methods are sensitive to ATRs and are robust in the presence of substitutions, insertions, and deletions
Sequencing technologies used to generate long strands of DNA are susceptible to laboratory errors that may result in several DNA nucleotides being deleted from the genome. Detecting such deletions in the protein coding regions is of utmost importance. Missing even a single nucleotide may lead to frame shifts with all the following codons (and consequently the encoded amino acids) being identified...
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