Related papers: Three phases in the evolution of the standard gene…
The quantum enveloping algebra U_q(sl(2) \oplus sl(2)) in the limit q \to 0 is proposed as a symmetry algebra for the genetic code. In this approach the triplets of nucleotids or codons in the DNA chain are classified in crystal bases,…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
We revisit the notion of gene regulatory code in embryonic development in the light of recent findings about genome spatial organisation. By analogy with the genetic code, we posit that the concept of code can only be used if the…
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.
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime…
Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…
A random-key genetic algorithm is an evolutionary metaheuristic for discrete and global optimization. Each solution is encoded as a vector of N random keys, where a random key is a real number randomly generated in the continuous interval…
We present a scenario for the origin of biological coding. In this context, coding is a semiotic relationship between chemical information stored in one location that links to chemical information stored in a separate location. Coding…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
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.
A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
The poly-tRNA model was recently presented for the origin and evolution of genetic coding. This model has led to a rather precise description of what might have occurred at the beginning of protein synthesis in the first life form. Here, we…
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…
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…
Generalized product codes (GPCs) are extensions of product codes (PCs) where coded bits are protected by two component codes but not necessarily arranged in a rectangular array. It has recently been shown that there exists a large class of…
The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of…