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The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…
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.…
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…
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…
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…
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…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In 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 problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…