Identification of repeats in DNA sequences using nucleotide distribution uniformity

DOI10.1016/J.JTBI.2016.10.013MaRDI QIDQ2013527zbMATH OpenOpenAlexWikidataFDO

Authors Changchuan Yin

Publication date 8 August 2017

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

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

zbMATH Keywords

DNA sequencegenomedistribution uniformityrepetitive elements

Mathematics Subject Classification ID

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

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.

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Cites work

• scientific article; zbMATH DE number 1149166 (Why is no real title available?)
• Detection and visualization of tandem repeats in dna sequences
• Information decomposition method to analyze symbolical sequences
• Periodic power spectrum with applications in detection of latent periodicities in DNA sequences
• Some features of Fourier spectrum for symbolic sequences

Cited in

(5)

• Latent periodicity-2 in coronavirus SARS-CoV-2 genome: evolutionary implications
• The statistical analysis of direct repeats in nucleic acid sequences
• scientific article; zbMATH DE number 2087058 (Why is no real title available?)
• DNADU
• Periodic power spectrum with applications in detection of latent periodicities in DNA sequences

Describes a project that uses

Uses Software

• RepeatMasker
• Python
• PPS
• GitHub

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