Nucleotide Frequencies in Human Genome and Fibonacci Numbers

Yamagishi, M. E. B.; Shimabukuro, Alex Itiro

doi:10.1007/s11538-007-9261-6

Cited by 48 publications

(36 citation statements)

References 9 publications

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“…Genomes are made of four nucleotides A, T, C, and G with an equal frequency between adenine and thymine as well as between cytosine and guanine, which is known as so-called Chargaff's first parity rule. For example, in humans, these four nucleotides were distributed as 29.55% A, 29.54% T, 20.44% C, and 20.46% G among a total of 2.86 3 10 9 bases (Zhao and Boerwinkle 2002), ranging from 26.05% A, 25.98% T, 23.98% C, and 23.97% G on chromosome 22 to 30.98% A, 31.18% T, 18.93% C, and 18.89% G on the Y chromosome (Yamagishi and Shimabukuro 2008). The mouse genome had 29.12% A, 29.14% T, 20.87% C, and 20.87% G in a total of 2.70 3 10 9 bases (Zhang and Zhao 2004).…”

Section: Discussionmentioning

confidence: 99%

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Jiang

Wu²,

Zhang

et al. 2008

Genetics

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Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A 1 Tcontent equals two at their immediate adjacent sites; and (3) C 4 Tand A 4 G transitions have reverse complementary neighborhood patterns and so do A 4 C and G 4 T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C 4 T/ A 4 G and A 4 C/G 4 T, the true neighborhood patterns for A 4 T and C 4 G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A 1 T and G 1 C was quite different. The ratio was lowest for C 4 G, but increased for C 4 T/A 4 G, further for A 4 C/G 4 T, and the most for A 4 T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A 4 G and C 4 T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for $20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.

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Section: Discussionmentioning

confidence: 99%

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Jiang

Wu²,

Zhang

et al. 2008

Genetics

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“…A C G T [ , , , ] ( Yamagishi and Shimabukuro, 2008), the entropy is calculated to be , , ] . If the nucleotides were uniformly distributed, the entropy would have achieved the highest value of 2 for a dictionary of size 4.…”

Section: Information Capacitymentioning

confidence: 99%

The information capacity of the genetic code: Is the natural code optimal?

Kuruoğlu

Arndt

2017

Journal of Theoretical Biology

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A B S T R A C TWe envision the molecular evolution process as an information transfer process and provide a quantitative measure for information preservation in terms of the channel capacity according to the channel coding theorem of Shannon. We calculate Information capacities of DNA on the nucleotide (for non-coding DNA) and the amino acid (for coding DNA) level using various substitution models. We extend our results on coding DNA to a discussion about the optimality of the natural codon-amino acid code. We provide the results of an adaptive search algorithm in the code domain and demonstrate the existence of a large number of genetic codes with higher information capacity. Our results support the hypothesis of an ancient extension from a 2-nucleotide codon to the current 3-nucleotide codon code to encode the various amino acids.

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“…Fibonacci numbers [18][19][20][21] have many implications in biological studies [22][23][24][25][26][27].…”

Section: Resultsmentioning

confidence: 99%

A Model-Based Approach for The Demonstration of Fermat’s Last Theorem

Xu¹

2017

PAMJ

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Abstract:Model-based approaches have many applications in bioinformatics studies. Fermat's last theorem is a theorem in number theory. This paper presented a model-based approach for the demonstration of Fermat's Last Theorem (FLT). Through the establishment of mathematical model, Fermat's Last Theorem (FLT) is converted into a problem for feasible solutions in linear programming. By prompting assumptions, and refuting the assumptions, it is demonstrated that Fermat's Last Theorem is right. The model-based approach for the demonstration of Fermat's Last Theorem (FLT) can assist scientific researchers in biological researches.

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Nucleotide Frequencies in Human Genome and Fibonacci Numbers

Cited by 48 publications

References 9 publications

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

The information capacity of the genetic code: Is the natural code optimal?

A Model-Based Approach for The Demonstration of Fermat’s Last Theorem

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