Related papers: The genetic code multiplet structure, in one numbe…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
Requiring stability of genetic code against translation errors, modelised by suitable mathematical operators in the crystal basis model of the genetic code, the main features of the organisation in multiplets of the mitochondrial and of the…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
We introduce an algorithm that conjectures the structure of a permutation class in the form of a disjoint cover of "rules"; similar to generalized grid classes. The cover is usually easily verified by a human and translated into an…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
It is presented that the positions of amino acids within Genetic Code Table follow from strict their physical and chemical properties as well as from a pure formal determination by the Golden mean.
The simple permutations in two permutation classes --- the 321-avoiding permutations and the skew-merged permutations --- are enumerated using a uniform method. In both cases, these enumerations were known implicitly, by working backwards…
Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
The idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…
We present a bijective algorithm with which an arbitrary permutation decomposes canonically into elementary blocks which we call families, which are sets with a specified number of ascents and descents. We show that families, arranged in an…
The Kronecker family of the genetic matrices is investigated, which is based on the genetic matrix [C T; A G], where C, T, A, G are the letters of the genetic alphabet. The matrix [C T; A G] in the second Kronecker power is the (4*4)-matrix…
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their…
The Higgs sector of the minimal 3 - 3 - 1 model with three triplets and one sextet is investigated in detail under the most general lepton--number conserving potential. The mass spectra and multiplet decompostion structure are explicitly…
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
A geometric grid class consists of those permutations that can be drawn on a specified set of line segments of slope \pm1 arranged in a rectangular pattern governed by a matrix. Using a mixture of geometric and language theoretic methods,…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…