Related papers: The multiplet structure of the genetic code, in on…
We study a construction, which produces surfaces $Y \subset P_3$ with cusps. For example we obtain surfaces of degree six with 18, 24 or 27 three-divisible cusps. For sextic surfaces in a particular family of up to 30 cusps the codes of…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Polynomial remainder codes are a large class of codes derived from the Chinese remainder theorem that includes Reed-Solomon codes as a special case. In this paper, we revisit these codes and study them more carefully than in previous work.…
A three-dimensional model of the genetic vocabulary is proposed in terms of determinative degree, an introduced characteristic of nucleotide, which reflects absolute difference between purin and pyrimidin bases in one DNA strand. In the…
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…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Using the correspondence between quadrics of ${\rm PG}(2,q)$ and points of ${\rm PG}(5,q)$, a family of $(6,q^3(q^2-1)(q-1)/3+(q^2+1)(q^2+q+1),4;3)_q$ constant dimension subspace codes is constructed.
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.…
Decoding the genome confers the capability to predict characteristics of the organism(phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly…
The structure of on-shell and off-shell 2D, (4,4) supersymmetric scalar multiplets is investigated, in components and in superspace. We reach the surprising result that there exist eight {\underline {distinct}} on-shell versions and an even…
In this paper, we develop the theory for constructing DNA cyclic codes of odd length over $R=\Z_4[u]/\langle u^2-1 \rangle$ based on the deletion distance. Firstly, we relate DNA pairs with a special 16 elements of ring $R$. Cyclic codes of…
For every group genetic code with finite number of generating and at most with one defining relation we introduce the braid group of this genetic code. This construction includes the braid group of Euclidean plane, the braid groups of…
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…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Reed--Solomon codes are a well--studied code class which fulfill the Singleton bound with equality. However, their length is limited to the size $q$ of the underlying field $\mathbb{F}_q$. In this paper we present a code construction which…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
Codes have been used for centuries to convey secret information.To a cryptanalyst, the interception of a code is only the first step in recovering a secret message.Deoxyribonucleic acid (DNA) is a biological and molecular code.Through the…