Related papers: Genetic Code: Four-Codon and Non-Four-Codon Degene…
Cyclic codes are among the most important families of codes in coding theory for both theoretical and practical reasons. Despite their prominence and intensive research on cyclic codes for over a half century, there are still open problems…
The matrix form of the presentation of the genetic code is described as the cognitive form to analyze structures of the genetic code. A similar matrix form is utilized in the theory of signal processing. The Kronecker family of the genetic…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
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…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
In this paper, some nonbinary quantum codes using classical codes over Gaussian integers are obtained. Also, some of our quantum codes are better than or comparable with those known before, (for instance [[8; 2; 5]]4+i).
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…
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…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…
The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…
Continuing our attempt to explain the degeneracy of the genetic code using basic classical Lie superalgebras, we present the branching schemes for the typical codon representations (typical 64-dimensional irreducible representations) of…
Quantum convolutional codes can be used to protect a sequence of qubits of arbitrary length against decoherence. In this paper, we give two new constructions of quantum MDS convolutional codes derived from generalized Reed-Solomon codes and…
Protein design is a technique to engineer proteins by modifying their sequence to obtain novel functionalities. In this method, amino acids in the sequence are permutated to find the low energy states satisfying the configuration. However,…
This paper is dealing with DNA cyclic codes which play an important role in DNA computing and have attracted a particular attention in the literature. Firstly, we introduce a new family of DNA cyclic codes over the ring…
Spatial fluctuations of guanine and cytosine base content (GC%) are studied by spectral analysis for the complete set of human genomic DNA sequences. We find that (i) the 1/f^alpha decay is universally observed in the power spectra of all…
The frequencies of A, C, G and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at four-fold degenerate sites respond directly to mutation pressure. At 1st and 2nd…
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…
We show how good quantum error-correcting codes can be constructed using generalized concatenation. The inner codes are quantum codes, the outer codes can be linear or nonlinear classical codes. Many new good codes are found, including both…
Generalized quasi-cyclic (GQC) codes form a natural generalization of quasi-cyclic (QC) codes. They are viewed here as mixed alphabet codes over a family of ring alphabets. Decomposing these rings into local rings by the Chinese Remainder…
Recently, researchers have applied genetic algorithms (GAs) to address some problems in quantum computation. Also, there has been some works in the designing of genetic algorithms based on quantum theoretical concepts and techniques. The so…