Identification of repeats in DNA sequences using nucleotide distribution uniformity

DOI10.1016/J.JTBI.2016.10.013zbMATH Open1368.92064arXiv1608.00567OpenAlexW2963064072WikidataQ36183616 ScholiaQ36183616MaRDI QIDQ2013527FDOQ2013527

Authors: Changchuan Yin 

Publication date: 8 August 2017

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive elements and periodicities of genomes is not clearly understood. We present an $extitabinitio$ method to quantitatively detect repetitive elements and infer the consensus repeat pattern in repetitive elements. The method uses the measure of the distribution uniformity of nucleotides at periodic positions in DNA sequences or genomes. It can identify periodicities, consensus repeat patterns, copy numbers and perfect levels of repetitive elements. The results of using the method on different DNA sequences and genomes demonstrate efficacy and accuracy in identifying repeat patterns and periodicities. The complexity of the method is linear with respect to the lengths of the analyzed sequences.

Full work available at URL: https://arxiv.org/abs/1608.00567

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zbMATH Keywords

DNA sequencegenomedistribution uniformityrepetitive elements

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Cites Work

• Title not available (Why is that?)
• Information decomposition method to analyze symbolical sequences
• Some features of Fourier spectrum for symbolic sequences
• Detection and visualization of tandem repeats in dna sequences
• Periodic power spectrum with applications in detection of latent periodicities in DNA sequences

Cited In (5)

• The statistical analysis of direct repeats in nucleic acid sequences
• Periodic power spectrum with applications in detection of latent periodicities in DNA sequences
• DNADU
• Latent periodicity-2 in coronavirus SARS-CoV-2 genome: evolutionary implications
• Title not available (Why is that?)

Uses Software

• RepeatMasker
• Python
• PPS
• GitHub

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