Sets generated by the genetic code

Kozlov, N. N.

doi:10.1134/s1064562408060136

Cited by 7 publications

(5 citation statements)

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“…This study was based on a mathematical analysis of all 5 possible overlap cases and relied on sets of so-called elementary genetic overlaps-e.o., or overlaps corresponding to a pair of single amino acids. In [6] a brief analysis of such sets is presented, and the final version in [2]. In Figure 1.…”

Section: Theorem For Homogeneous Overlapsmentioning

confidence: 99%

“…For the proof we successively substitute each of the representation (6) in u3: (7) where n'i is the single component of the set Ni, where i∈ (1,6), and the string na.-nucleotide sequences that are formed after this substitution. In the first case, in (3), the base codon n1n1n1 was used for encoding amino acid Ama from the bottom position, in the second-n2n2n2-from the middle position, and in the third-n3n3n3-from the top position.…”

Section: Theorem For Homogeneous Overlapsmentioning

confidence: 99%

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Computation of the Genetic Code: Full Version

Kozlov¹

2017

JCC

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One of the problems in the development of mathematical theory of the genetic code (summary is presented in [1], the detailed-to [2]) is the problem of the calculation of the genetic code. Similar problem in the world is unknown and could be delivered only in the 21st century. One approach to solving this problem is devoted to this work. For the first time a detailed description of the method of calculation of the genetic code was provided, the idea of which was first published earlier [3]), and the choice of one of the most important sets for the calculation was based on an article [4]. Such a set of amino acid corresponds to a complete set of representation of the plurality of overlapping triple gene belonging to the same DNA strand. A separate issue was the initial point, triggering an iterative search process all codes submitted by the initial data. Mathematical analysis has shown that the said set contains some ambiguities, which have been founded because of our proposed compressed representation of the set. As a result, the developed method of calculation was reduced to two main stages of research, where at the first stage only single-valued domains were used in the calculations. The proposed approach made it possible to significantly reduce the amount of computation at each step in this complex discrete structure.

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Section: Theorem For Homogeneous Overlapsmentioning

confidence: 99%

Section: Theorem For Homogeneous Overlapsmentioning

confidence: 99%

Computation of the Genetic Code: Full Version

Kozlov¹

2017

JCC

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Section: Theorem For Homogeneous Overlapsmentioning

confidence: 99%

“…For the proof we successively substitute each of the re.o.resentations (6) Where n'i is the single component of the set Ni, where i (1,6), and the string na. -nucleotide sequences that are formed after this substitution.…”

Section: Solution Of the Problemmentioning

confidence: 99%

Computation of the genetic code

Kozlov¹,

Kozlova²

2017

Fifth International Conference on Advances in Bio-Informatics, Bio-Technology and Environmental Engineering - ABBE 2017

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“…Overlapping genes are cases where the same segment of DNA encodes more than one (up to 6) protein sequence. During the studies, a number of problems for the area of DNA with overlaps of genes had been solved: the strictness of the degree of the relation of protein sequences and this area [1,2]; the role of irregularities in the code [3]; the relevance of each notional codon [4]; the method for constructing any overlap of gene pairs from one strand of DNA [5,6]; reducing the size of the genome, due to deviations of code from its standard structure [7]; the mathematical analysis of all five methods of paired overlaps of genes for the standard deviant code [8], as well as for all 14 deviant codes [9]; the introduction of integral characteristics of the code for both overlapping and nonoverlapping genes and the determination of their interrelation [10][11][12][13]; the establishment of the mathematical analogy of genetic overlaps and stems of the secondary structure of mRNAs [12], the theory of elementary genetic overlaps [14]; as well as the role of ambiguities in sets of such overlaps [15]. A detailed exposition of these problems in their interrelation is presented in the author's monograph [16].…”

mentioning

confidence: 99%

Computation of the genetic code

Kozlov

2012

Math Models Comput Simul

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The author has conducted mathematical analysis of genetic decoding for a number of years. Overlapping genes, discovered in 1976, were one of the main objects of the study. These are cases where the same segment of DNA encodes two or more protein sequences. Numerous cases of identi fied genetic overlaps allowed setting a number of mathematical problems that have been successfully solved. A detailed exposition of these problems is given in the author's monograph Mathematical Anal ysis of Genetic Code (BINOM, Moscow, 2010). Such problems have made it possible to penetrate deeply enough into the structure of the genetic code and its relationship with the overlapping genes. As a result, a new problem was set: the computation of the genetic code on the basis of the amino acid sequences that record overlapping genes. One approach to this problem is described in this paper.

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Sets generated by the genetic code

Cited by 7 publications

References 5 publications

Computation of the Genetic Code: Full Version

Computation of the Genetic Code: Full Version

Computation of the genetic code

Computation of the genetic code

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