Related papers: Genetic Code: A New Understanding of Codon - Amino…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
Information is often encoded as an aperiodic chain of building blocks. Modern digital computers use bits as the building blocks, but in general the choice of building blocks depends on the nature of the information to be encoded. What are…
This paper is devoted to a new classification of the twenty amino acids based on the heronian (integer) tetrahedron.
The biological distinction between the base positions in the codon, the chemical types of bases (purine and pyrimidine) and their hydrogen bond number have been the most relevant codon properties used in the genetic code analysis. Now,…
The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
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…
In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
Part 1 of the study intends to show that the universal trend of amino acid gain and loss discovered by Jordan et al. (2005) can be accounted for by the spontaneity of DNA typical damages. These damages lead to replacements of guanine and…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
A new n-dimensional vector space of the DNA sequences on the Galois field of the 64 codons (GF(64)) is proposed. In this vector space gene mutations can be considered linear transformations or translations of the wild type gene. In…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…