Related papers: DNA coding and G\"odel numbering
Three steps aid in the analysis of selection. First, describe phenotypes by their component causes. Components include genes, maternal effects, symbionts, and any other predictors of phenotype that are of interest. Second, describe fitness…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
The idea of computing with DNA was given by Tom Head in 1987, however in 1994 in a seminal paper, the actual successful experiment for DNA computing was performed by Adleman. The heart of the DNA computing is the DNA hybridization, however,…
Biomolecular computation has emerged as an important area of computer science research due to its high information density, immense parallelism opportunity along with potential applications in cryptography, genetic engineering and…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition.…
We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…
We define a general class of models representing natural selection between two alleles. The population size and spatial structure are arbitrary, but fixed. Genetics can be haploid, diploid, or otherwise; reproduction can be asexual or…
DNA sequencing allows for the determination of the genetic code of an organism, and therefore is an indispensable tool that has applications in Medicine, Life Sciences, Evolutionary Biology, Food Sciences and Technology, and Agriculture. In…
Natural supports of information are given by random copolymers such as DNA or RNA where information is coded in the sequence of covalent bonds. At the molecular scale, the stochastic growth of a single copolymer with or without a template…
Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and…
Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. Families of genetic (4*4)- and (8*8)-matrices show unexpected connections of the genetic system…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
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…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
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…