Detection of Tandem Repeats in DNA Sequences Using Short-Time Ramanujan Fourier Transform

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 19; no. 3; pp. 1583 - 1591
• Main Authors: Yadav, Yashpal, Sharma, Sanjeev Narayan, Shakya, Devendra Kumar
• Format: Journal Article
• Language: English
• Published: United States IEEE 01-05-2022; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Algorithms; Base Sequence; Bioinformatics; Computer applications; Deoxyribonucleic acid; Discrete Fourier transforms; DNA; Electronic mail; Forensic science; Fourier Analysis; Fourier transforms; Gene sequencing; Genetic disorders; Genomic sequence; Genomics; Humans; Nucleotide sequence; Nucleotides; Ramanujan fourier transform; Sequence Analysis, DNA - methods; Signal processing algorithms; Spectrogram; Tandem Repeat Sequences - genetics; tandem repeats
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2021.3053656

Tandem repeats in genomic sequences are characterized by two or more contiguous copies of a pattern of nucleotides. The role of these repeats as molecular markers is well established in various genetic disorders, human evolution studies, DNA forensics and intron retention. In this work a computational method has been developed for the extraction of both exact and approximate tandem repeats. The proposed algorithm uses Ramanujan Fourier Transform (RFT) to identify periodicities in the DNA sequences. Since RFT estimates the period directly, rather than inferring it from the signal's spectrum, it provides a more sensitive and rapid detection of tandem repeats as compared to other available popular computational methods.