Related papers: Genetic Code Table: A note on the three splittings…
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…
What are proteins made from, as the working parts of the living cells protein machines? To answer this question, we need a technology to disassemble proteins onto elementary func-tional details and to prepare lumped description of such…
This issue includes six articles that develop and apply statistical methods for the analysis of gene sequencing data of different types. The methods are tailored to the different data types and, in each case, lead to biological insights not…
The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…
The set of known dialects of the genetic code (GC) is analyzed from the viewpoint of the genetic octave Yin-Yang-algebra. This algebra was described in the previous author's publications. The algebra was discovered on the basis of…
The numbers of natural chemical elements, minerals, inorganic and organic chemical compounds are determined by 1, 2, 3 and 4-combinations of a set 95 and are respectively equal to 95, 4,465, 138,415 and 3,183,545. To explain these relations…
This paper reports about an approach to the classification of proteins' primary structures taking advantage of the Self Organizing Maps algorithm and of a numerical coding of the aminoacids based upon their physico-chemical properties.…
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…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
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…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
The Golden Code is a full-rate full-diversity space-time code, which achieves maximum coding gain for Multiple-Input Multiple-Output (MIMO) systems with two transmit and two receive antennas. Since four information symbols taken from an…
We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino…
A pattern Recognition of a probability distribution of amino acids is obtained for selected families of proteins. The mathematical model is derived from a theory of protein families formation which is derived from application of a Pauli's…
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…
To synthesize peptides alongside the RNAs making the so-called RNA world, some genetic coding involving RNA had to develop. Herein, it is proposed that the first real-coding setup was a direct one, made up of continuous poly-tRNA-like…
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…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
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…