Related papers: A Binary Representation of the Genetic Code
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 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…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…
This paper describes a new method of data encoding which may be used in various modern digital, computer and telecommunication systems and devices. The method permits the compression of data for storage or transmission, allowing the exact…
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…
A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
The algebraic structures of the genetic code are most important to obtain additional information about the semantic code and its applications. In this paper we define two dual Boolean codon lattices of the genetic code using hydrogen bond…
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.
Motivation: Proteins are known to undergo conformational changes in the course of their functions. The changes in conformation are often attributable to a small fraction of residues within the protein. Therefore identification of these…
The tree based representation described in this paper, hereditarily binary numbers, applies recursively a run-length compression mechanism that enables computations limited by the structural complexity of their operands rather than by their…
In the present work, 16 genetic code doublets and their cognate amino acids in the genetic code are fitted into a polyhedron model. Based on the structural regularity in nucleobases, and by using a series of common-sense topological…
This short note introduces a geometric representation for binary (or ternary) sequences. The proposed representation is linked to multivariate data plotting according to the radar chart. As an illustrative example, the binary Hamming…
By starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient subspaces of the…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
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,…