Related papers: Gene Algebra from a Genetic Code Algebraic Structu…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
We propose a new geometrical model of matter, in which neutral atoms are modelled by compact, complex algebraic surfaces. Proton and neutron numbers are determined by a surface's Chern numbers. Equivalently, they are determined by…
The insertion of HIV and other DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of these insertions are not random and occupy specific positions within the genome but the physical mechanisms…
Let H be a Hopf algebra, A a left H-module algebra and V a left H-module A-bimodule. We study the behavior of the right A-linear endomorphisms of V under twist deformation. We in particular construct a bijective quantization map to the…
Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
Imposing a minimum principle in the framework of the so called crystal basis model of the genetic code, we determine the structure of the minimum set of 22 anticodons which allows the translational-transcription for animal mitochondrial…
We introduce a procedure based on computational algebraic geometry to determine whether two algebras are isomorphic. We then apply it to show that if $R$ is a commutative unital ring in which $2$ is not invertible, $G$ is a group of order…
DNA segments and sequences have been studied thoroughly during the past decades. One of the main problems in computational biology is the identification of exon-intron structures inside genes using mathematical techniques. Previous studies…
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…
In this article we study the endomorphism algebras of abelian varieties $A$ defined over a given number field $K$ with large cyclic 2-torsion fields. A key step in doing so is to provide criteria for all the endomorphisms of $A$ to be…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
This paper considers a new alphabet set, which is a ring that we call $\mathbb{F}_4R$, to construct linear error-control codes. Skew cyclic codes over the ring are then investigated in details. We define a nondegenerate inner product and…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
We investigate algorithms for encoding of one-point algebraic geometry (AG) codes over certain plane curves called $C_{ab}$ curves, as well as algorithms for inverting the encoding map, which we call "unencoding". Some $C_{ab}$ curves have…
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…
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…
A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF(64)) was recently presented. Now, in order to include deletions and insertions (indel mutations), we have defined a new Galois field over the set…