Identification of repeats in DNA sequences using nucleotide distribution uniformity

Yin, Changchuan

doi:10.1016/j.jtbi.2016.10.013

Cited by 7 publications

(6 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This approach has been implemented for example in RepeatScout [59], REPuter [60], SPADE [61], WindowMasker [62], Vmatch [63], phRAIDER [64]. Fourier transforms based algorithms are implemented for example in nucleotide-based software Spectral Repeat Finder [65] and SBARS [66] and dinucleotide-based DNADU [67]. It is of note that Fourier power spectrum may not characterize repeats precisely due to the inability to identify repetitive pattern, copy number and the level of degeneration.…”

Section: Introductionmentioning

confidence: 99%

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

et al. 2019

View full text Add to dashboard Cite

Background Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA. Results We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats. Conclusions ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/ . It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research.

show abstract

Section: Introductionmentioning

confidence: 99%

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

et al. 2019

View full text Add to dashboard Cite

show abstract

“…To inspect the insightful traits of the SARS-CoV-2 genome, we utilize our periodicity analysis method to survey the nucleotide distributions and the rendered periodicities in the genome. We previously proposed the periodicity analysis method to quantitatively detect the nucleotide repeats and periodicities in a genome (Yin, 2017). The method employs nucleotide distributions on periodic positions in a genome and identifies approximate repeat structures as the signatures of the genome.…”

Section: Concepts and Methodsmentioning

confidence: 99%

“…The method employs nucleotide distributions on periodic positions in a genome and identifies approximate repeat structures as the signatures of the genome. Because we have included more functionalities, such as smoothing the periodicity profile, from the original method, here we describe the method in detail though the technical algorithms had been delineated previously (Yin, 2017). Our computer programs of the periodicity analysis of a genome are available to the public at GitHub repository https://github.com/cyinbox/DNADU.…”

Section: Concepts and Methodsmentioning

confidence: 99%

“…The nucleotide distributions at the periodic positions of a DNA sequence can be represented by a congruence derivative (CD) vector (Yin and Wang, 2016;Yin, 2017). The CD vector of a nucleotide for a specific periodicity is constructed by the cumulative frequencies of the nucleotide at these periodic positions (Definition 2.1).…”

Section: Periodic Nucleotide Frequencies In a Dna Sequencementioning

confidence: 99%

See 1 more Smart Citation

Dinucleotide repeats in coronavirus SARS-CoV-2 genome: evolutionary implications

Yin

2020

Preprint

Self Cite

View full text Add to dashboard Cite

The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little is known of the intrinsic organization and evolution of the genome. To this end, we present a mathematical method for the genomic spectrum, a kind of barcode, of SARS-CoV-2 and common human coronaviruses. The genomic spectrum is constructed according to the periodic distributions of nucleotides, and therefore reflects the unique characteristics of the genome. The results demonstrate that coronavirus SARS-CoV-2 exhibits dinucleotide TT islands in the non-structural proteins 3, 4, 5, and 6. Further analysis of the dinucleotide regions suggests that the dinucleotide repeats are increased during evolution and may confer the evolutionary fitness of the virus. The special dinucleotide regions in the SARS-CoV-2 genome identified in this study may become diagnostic and pharmaceutical targets in monitoring and curing the COVID-19 disease.

show abstract

“…A DNA sequence is a nonperiodic signal with some periodic repetitive parts. 32 Because spectral transforms are intended to transform periodic signals, transforming nonperiodic signals into signal spectra may resemble hashing one representation to another without understanding its internal structure. The intuition is that the transform helps to find variations in the density of particular characters inside a sequence.…”

Section: Introductionmentioning

confidence: 99%

SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal Processing Approaches

Farkaš

Sitarčík

Brejová

et al. 2019

Evol Bioinform Online

View full text Add to dashboard Cite

Computing similarity between 2 nucleotide sequences is one of the fundamental problems in bioinformatics. Current methods are based mainly on 2 major approaches: (1) sequence alignment, which is computationally expensive, and (2) faster, but less accurate, alignment-free methods based on various statistical summaries, for example, short word counts. We propose a new distance measure based on mathematical transforms from the domain of signal processing. To tolerate large-scale rearrangements in the sequences, the transform is computed across sliding windows. We compare our method on several data sets with current state-of-art alignment-free methods. Our method compares favorably in terms of accuracy and outperforms other methods in running time and memory requirements. In addition, it is massively scalable up to dozens of processing units without the loss of performance due to communication overhead. Source files and sample data are available at https://bitbucket.org/fiitstubioinfo/swspm/src

show abstract

Identification of repeats in DNA sequences using nucleotide distribution uniformity

Cited by 7 publications

References 22 publications

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

Dinucleotide repeats in coronavirus SARS-CoV-2 genome: evolutionary implications

SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal Processing Approaches

Contact Info

Product

Resources

About