Related papers: Genetic Code Table: A note on the three splittings…
Overlapping genes exist in all domains of life and are much more abundant than expected at their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading…
The concepts of alpha- and beta-packets of the periodic table of chemical elements and chemical compounds are defined. The first of the 47 minerals alpha-packets is composed. In it all minerals are arranged in increasing Iav index of…
Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be…
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…
The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional…
Abundances of 18 chemical elements have been derived for 27 A/Am and 16 F stars members of the Pleiades and Coma Berenices open clusters. We have specifically computed, with the Montr\'eal code, a series of evolutionary models for two A…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
Algebraic properties of the genetic code are analyzed. The investigations of the genetic code on the basis of matrix approaches ("matrix genetics") are described. The degeneracy of the vertebrate mitochondria genetic code is reflected in…
In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
We discuss the similarity of the degeneration structure of the genetic code with a pure number theoretic -- ``divisors code.'' The most interesting thing about our observation is not that there is a connection between number theory and the…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
The genetic product of the groupoids, originating in the theory of DNA recombination, is introduced. It permits a natural generalization of the classical genetic algorithm. The full characterization of all three-element genetic groupoids…
The mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
We will describe an algorithm to arrange all the positive and negative integer numbers. This array of numbers permits grouping them in six different Classes, $\alpha$, $\beta$, $\gamma$, $\delta$, $\epsilon$, and $\zeta$. Particularly,…
The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…
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 classification of amino acids and their sequence analysis plays a vital role in life sciences and is a challenging task. This article uses and compares state-of-the-art deep learning models like convolution neural networks (CNN), long…
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,…