Identification of exon regions in eukaryotes using fine-tuned variational mode decomposition based on kurtosis and short-time discrete Fourier transform

• Published in: Nucleosides, nucleotides & nucleic acids nucleotides & nucleic acids, 2024-08, p.1-24
• Main Authors: Jayasree, K, Kumar Hota, Malaya, Dwivedi, Atul Kumar, Ranjan, Himanshuram, Srivastava, Vinay Kumar
• Format: Article
• Language: English
• ISSN: 1525-7770; 1532-2335; 1532-2335
• DOI: 10.1080/15257770.2024.2388785

In genomic research, identifying the exon regions in eukaryotes is the most cumbersome task. This article introduces a new promising model-independent method based on short-time discrete Fourier transform (ST-DFT) and fine-tuned variational mode decomposition (FTVMD) for identifying exon regions. The proposed method uses the /3 periodicity property of the eukaryotic genes to detect the exon regions using the ST-DFT. However, background noise is present in the spectrum of ST-DFT since the sliding rectangular window produces spectral leakage. To overcome this, FTVMD is proposed in this work. VMD is more resilient to noise and sampling errors than other decomposition techniques because it utilizes the generalization of the Wiener filter into several adaptive bands. The performance of VMD is affected due to the improper selection of the penalty factor ( ), and the number of modes ( ). Therefore, in fine-tuned VMD, the parameters of VMD ( and ) are optimized by maximum kurtosis value. The main objective of this article is to enhance the accuracy in the identification of exon regions in a DNA sequence. At last, a comparative study demonstrates that the proposed technique is superior to its counterparts.