On comparing composition principles of long DNA sequences with those of random ones

Fimmel, Elena; Gumbel, Markus; Karpuzoglu, Ali; Petoukhov, Sergey V.

doi:10.1016/j.biosystems.2019.04.003

Cited by 11 publications

(7 citation statements)

References 16 publications

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“…For example, in the human genome, about a third of DNA sequences are represented by complementary palindromes [Gusfield, 1997;McConkey, 1993]. In evolutionary biology, the abundance of such complementary palindromes in genomes is seen as evidence of not random DNA sequences, that is, their irreducibility to a set of random mutations (see additional data in [Fimmel, Gumbel, Karpuzoglu, Petoukhov, 2019;Petoukhov, Tolokonnikov, 2020]).…”

Section: Introductionmentioning

confidence: 99%

“…For long nucleotide sequences of single-stranded DNA, the second Chargaff's rule is well known, which states that in such sequences the amount of guanine G is approximately equal to the amount of cytosine C and the amount of adenine A is approximately equal to the amount of thymine T. Many authors have devoted their works to the analysis and discussion of this rule (see, for example, [Fimmel, Gumbel, Karpuzoglu, Petoukhov, 2019;Prabhu, 1993;Rapoport, Trifonov, 2012;Rosandic, Vlahovic, Gluncic, Paar, 2016;Shporer, Chor, Rosset, and Horn, 2016;Yamagishi, 2017]). According to [Albrecht-Buehler, 2006], this rule applies to the eukaryotic chromosomes, the bacterial chromosomes, the double-stranded DNA viral genomes, and the archaeal chromosomes provided they are long enough.…”

Section: Introductionmentioning

confidence: 99%

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Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

Petoukhov¹

2020

Preprint

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The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method are shown to the analysis of the following long sequences: 1) amino acid sequences in long proteins like the protein Titin; 2) phonetic sequences of long Russan literary texts (for checking of thoughts of many authors that phonetic organization of human languages is deeply connected with the genetic language). The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

Petoukhov¹

2020

Preprint

Self Cite

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show abstract

“…For example, in the human genome, about a third of DNA sequences are represented by complementary palindromes ( Gusfield, 1997 ; McConkey, 1993 ). In evolutionary biology, the abundance of such complementary palindromes in genomes is seen as evidence of not random DNA sequences, that is, their irreducibility to a set of random mutations (see additional data in ( Fimmel et al, 2019 ; Petoukhov, Tolokonnikov, 2020 )).…”

Section: Introductionmentioning

confidence: 99%

“…For long nucleotide sequences of single-stranded DNA, the second Chargaff's rule is well known, which states that in such sequences the amount of guanine G is approximately equal to the amount of cytosine C and the amount of adenine A is approximately equal to the amount of thymine T. Many authors have devoted their works to the analysis and discussion of this rule (see, for example ( Fimmel et al, 2019 ; Prabhu, 1993 ; Rapoport, Trifonov, 2012 ; Rosandic et al, 2016 ; Shporer et al, 2016 ; Yamagishi, 2017 ),). According to ( Albrecht-Buehler, 2006 ), this rule applies to the eukaryotic chromosomes, the bacterial chromosomes, the double-stranded DNA viral genomes, and the archaeal chromosomes provided they are long enough.…”

Section: Introductionmentioning

confidence: 99%

Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes

Petoukhov

2020

Biosystems

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The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for the cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/ n . These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The results concerns additionally the problem of the origin of life. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method is shown to the analysis of amino acid sequences in long proteins like the protein Titin. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.

show abstract

Section: Introductionmentioning

confidence: 99%

Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

Petoukhov¹

2020

Preprint

Self Cite

View full text Add to dashboard Cite

The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of rhythmically repeating deviations from model hyperbolic sequences; these deviations are associated with DNA triplets and should be systematically analyzed for a deeper understanding the genetic coding system. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.

show abstract

On comparing composition principles of long DNA sequences with those of random ones

Cited by 11 publications

References 16 publications

Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes

Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

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