Related papers: Genetic Code: A New Understanding of Codon - Amino…

New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…

This letter reports complete sets of two-fold symmetries between partitions of the universal genetic code. By substituting bases at each position of the codons according to a fixed rule, it happens that properties of the degeneracy pattern…

We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage…

The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…

A novel approach to protein multiple sequence alignment is discussed: substantially this method counterparts with substitution matrix based methods (like Blosum or PAM based methods), and implies a more deterministic approach to…

Protein-fragment seqlets typically feature about 10 amino acid residue positions that are fixed to within conservative substitutions but usually separated by a number of prescribed gaps with arbitrary residue content. By quantifying a…

Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…

All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick…

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 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…

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 standard genetic code multiplet structure as well as the correct degeneracies, class by class, are all extracted from the (unique) number 23, the order of the permutation group of 23 objects.

This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2grams are offered as an alternative to…

The frequencies of A, C, G and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at four-fold degenerate sites respond directly to mutation pressure. At 1st and 2nd…

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…

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…

Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…

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…

Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…