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Detection of periodicity in symbolic sequences such as DNA is of considerable interest in a number of applications, however fast, accurate algorithms are needed for measuring spectral content at multiple integer periods. This paper describes an integer period discrete Fourier transform (IPDFT), presents a new algorithm for its implementation, and discusses applications to DNA sequence analysis. Evaluations...
In this paper, we firstly investigate the effect of window lengths on selected signal processing-based gene and exon prediction methods. We then optimize these methods to improve their prediction accuracy by employing the best DNA representation, a suitable window length, and boosting the output signals to enhance protein coding and suppress the non-coding regions. It is shown herein that the proposed...
A technique for increasing the discrimination between coding and non-coding regions of a DNA sequence during exon prediction is presented, based upon the boosting method employed in speech enhancement. The proposed method improves the likelihood of correctly identifying coding regions compared with existing genomic signal processing techniques, such as the DFT, IIR anti-notch filter, and multi-stage...
In this paper, we propose the novel use of an autoregressive (AR) model to produce a multi-dimensional feature for distinguishing between genomic protein coding and non-coding regions, at their nucleotide level. In contrast to previous research, in which AR models were used to estimate a single frequency, here AR model parameters characterizing the entire short-term sequence spectrum are employed...
This paper presents the signal boosting technique for gene and exon identification of a DNA sequence. Newly proposed signal boosting technique is used to enhance the coding region and improve the likelihood of correctly identifying the coding region. This new method is compared with other genomic signal processing techniques, such as DFT, IIR anti-notch filter, and multistage filters. Results show...
Processing of DNA sequences using traditional digital signal processing methods requires their conversion from a character string into numerical sequences as a first step. Many representations introduced previously assign values to indicate the four DNA nucleotides A, C, G, and T that impose mathematical structures not present in the actual DNA sequence. In this paper, almost all existing methods...
The detection of period-3 components in exons of eukaryotic gene sequences enables signal processing based time-domain and frequency-domain methods to predict these regions. In this paper, we improve the prediction accuracy of frequency-domain methods by proposing a new algorithm known as the paired and weighted spectral rotation (PWSR) measure, which exploits both period-3 behaviour and another useful...
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