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In the paper, the performances on FFT-based, FIR and IIR digital filter-based (DF-based) period-3 classifications of short exon and intron sequences of the human and eleven model organisms are studied. For each organism, sequences of 150-base length are chosen and 16,000 sequences are used for training and testing. FIR and IIR digital filter orders are chosen to be around a similar level of computational...
In spite of the recent development of computational methods for human promoter prediction, the prediction performance still needs improvement. In particular, the high false positive rate of the traditional approaches decreases the prediction reliability and leads to erroneous results in gene annotation. To improve the prediction accuracy and reliability, a DNA numerical representation and neural network...
Promoter recognition in various organisms is an area of interest in bioinformatics. In this paper, a feed-forward neural network classifier is presented to predict promoters in three organisms using a DNA numerical representation approach. The proposed system was found to be able to predict promoters with a sensitivity of 87%, 87%, 99% while reducing false prediction rate for non-promoter sequences...
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...
The sequencing of genomic data requires methods to allow this data to be visualized and analyzed. With the emergence of genomic signal processing, graphical representation techniques play a key role in applying digital signal processing techniques like Fourier transforms, and more recently, wavelet transform for visualizing DNA sequence. The choice of the graphical representation technique for a DNA...
DNA sequence analysis using digital signal processing requires conversion of a base sequence to a numerical sequence. The choice of the numerical representation of a DNA sequence affects how well its biological properties can be reflected in the numerical domain for the detection and identification of the characteristics of special regions of interest. This paper presents some selected methods of...
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