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<p>Repetitive elements play a significant role in deciding the functionality of the DNA. Their association with neurodegenerative diseases, leprosy, and cancer is now well established. They are also useful in the investigation of human identity, parental testing, phylogenetic studies, forensic science, DNA fingerprinting, and crime scene investigation. Their emerging role in the functionality of the non-coding RNAs (ncRNAs) further makes them more important. Tandem repeats (TRs) are an important subclass of the repetitive elements and therefore many computational methods for their identification have been developed. These methods can be broadly classified as library-based and the <i>de novo</i> methods. In this paper, an exhaustive review of the signal processing (SP) based <i>de novo</i> methods for the detection of the tandem repeats has been done. This paper critically examines the reported SP methods for the TR detection based on—(i) mapping schemes, (b) total number of detections, (c) the types of TRs detected, (d), computational complexity, and (e) accuracy. This comparative study can guide in the selection of the appropriate method as well as help in the development of some new algorithms addressing the existing limitations.</p>

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Identification of Tandem Repeats in DNA Sequences Using Signal Processing Algorithms: A Review

  • 期刊论文

  • 发表日期：

    2025年9月2日

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  • Sunil Datt Sharma,
  • Yashpal Yadav,
  • Sanjeev Narayan Sharma

摘要

Repetitive elements play a significant role in deciding the functionality of the DNA. Their association with neurodegenerative diseases, leprosy, and cancer is now well established. They are also useful in the investigation of human identity, parental testing, phylogenetic studies, forensic science, DNA fingerprinting, and crime scene investigation. Their emerging role in the functionality of the non-coding RNAs (ncRNAs) further makes them more important. Tandem repeats (TRs) are an important subclass of the repetitive elements and therefore many computational methods for their identification have been developed. These methods can be broadly classified as library-based and the de novo methods. In this paper, an exhaustive review of the signal processing (SP) based de novo methods for the detection of the tandem repeats has been done. This paper critically examines the reported SP methods for the TR detection based on—(i) mapping schemes, (b) total number of detections, (c) the types of TRs detected, (d), computational complexity, and (e) accuracy. This comparative study can guide in the selection of the appropriate method as well as help in the development of some new algorithms addressing the existing limitations.