Detection of short exons in DNA sequences using complex wavelet transform of structural features

Abstract

The paper presents a spectral method used for detection of short coding regions in genes. The complex representation of four nucleotides involving three basic chemical and structural properties is used for conversion of a symbolic sequence into a genomic signal. Another genomic signal is generated from dinucleotide propeller twist. Filtered complex combination of both signals is transformed by a complex continuous wavelet transform. Its results were analysed both in amplitude and phase parts. Experimental results obtained by this method are shown to be comparable or better than recently published methods based on the selected set of genes.Index Terms-Exon detection, DNA structure, wavelet analysis, DNA sequence analysis.

Exon Mapping in Long Noncoding RNAs Using Digital Filters

“… 16 , 17 , 19 It was observed in noncoding regions for prokaryotes and some viral and mitochondrial base sequences 2 decades ago, 24 and this concept is explored here. There are other signal processing–based automated methods 32 , 33 to detect exons in coding regions. One such method 32 detects short exons in DNA sequences by analyzing their structural properties, namely, DNA bending stiffness, disrupt energy, free energy, and propeller twist making use of the autoregressive model to arrive at linear prediction matrices for these features.…”

“…Short exons have also been detected by evaluating the complex wavelet transform of the structural features of DNA sequences. 33 The authors opted for period 3 property because of its proven robustness and relative simplicity. 16 , 17 , 19 …”

Differential Analysis of Neurodegenerative Aging-Related Mitochondrial Genes of Long-Lived Naked Mole-Rat

“…Mitochondrial Nucleotide Genomic Signals (mtNuGSs) for various species have been analyzed comparatively, since the conversion of nucleotide sequences to Nucleotide Genomic Signals (NuGSs) allows to process them as digital signals [8], [9].…”