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Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…

Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…

The ratios of the codon usage in the quartets and sextets for the vertebrate series exhibit a correlated behaviour which fits naturally in the framework of the crystal basis model of the genetic code. Moreover the observed universal…

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…

The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…

We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the…

The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…

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…

Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…

The usage frequencies for codons belonging to quartets are analized, over the whole exonic region, for 92 biological species. Correlation is put into evidence, between the usage frequencies of synonymous codons with third nucleotide A and C…

A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…

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 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…

Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…

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…

The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…

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…

This article is interested in the origin of the genetic code, it puts forward a scenario of a simultaneous selection of the bases and amino acids and setting up of a correlation between them. Each amino acid is associated with a pair of its…

The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…