Related papers: Three phases in the evolution of the standard gene…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
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…
Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal.…
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching…
The advent of neural audio codecs has increased in popularity due to their potential for efficiently modeling audio with transformers. Such advanced codecs represent audio from a highly continuous waveform to low-sampled discrete units. In…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
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…
Modelising the translation errors by suitable mathematical operators in the crystal basis model of the genetic code and requiring that codons prone to be misread encode the same amino-acid, the main features of the organisation in…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
A new n-dimensional vector space of the DNA sequences on the Galois field of the 64 codons (GF(64)) is proposed. In this vector space gene mutations can be considered linear transformations or translations of the wild type gene. In…
Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
ECG heartbeat classification plays a vital role in diagnosis of cardiac arrhythmia. The goal of the Physionet/CinC 2021 challenge was to accurately classify clinical diagnosis based on 12, 6, 4, 3 or 2-lead ECG recordings in order to aid…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
This paper presents, for the first time, four diversity types of protein amino acids. The first type includes two amino acids (G, P), both without standard hydrocarbon side chains; the second one four amino acids, as two pairs [(A, L), (V,…