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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...
Due to the enormous amount of data in DNA sequences to be processed, the computational complexity and speed are important issues to be considered. In this paper, a new integrative method is presented for predicting protein coding regions. We first establish a Takagi-Sugeno fuzzy model to identify the first nucleotide of a codon in coding regions, then the time-frequency characteristics of the output...
Many signal processing techniques were proposed in the past to identify the so-called period-3 component in the protein coding regions of DNA sequences. Most of these methods evaluate the magnitude of the output of an M-point sliding window DFT at the frequency k = M/3. In this paper, we introduce a new multirate DSP approach that computes the phase of the output of the sliding window DFT at the above...
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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