Related papers: The genetic code, 8-dimensional hypercomplex numbe…
Codes from generalized Hadamard matrices have already been introduced. Here we deal with these codes when the generalized Hadamard matrices are cocyclic. As a consequence, a new class of codes that we call generalized Hadamard full…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
We describe a genetic algorithm to find candidates for $h^*$-vectors satisfying given properties in the space of integers vectors of finite length. We use an implementation of such algorithm to find a 52-dimensional lattice polytope having…
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime…
A haplotype block, or simply a block, is a chromosomal segment, DNA base sequence or string that occurs in only a few variants or types in the genomes of a population of interest, and that has an encapsulated or 'private' frequency…
We propose a generic framework to describe classical Ising-like models defined on arbitrary graphs. The energy spectrum is shown to be the Hadamard transform of a suitably defined sparse "coding" vector associated with the graph. We expect…
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…
A method for automatically finding a program (bytecode) realizing the given algorithm is developed. The algorithm is specified as a set of tests (input\_data) $ \rightarrow $ (output\_data). Genetic methods made it possible to find the…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Let k be a field of characteristic zero. We consider graded subalgebras A of k[x_1,...,x_m]/(x_1^2,...,x_m^2) generated by d linearly independant linear forms. Representations of matroids over k provide a natural description of the…
The $\mathbb{Z}_2\mathbb{Z}_4\mathbb{Z}_8$-additive codes are subgroups of $\mathbb{Z}_2^{\alpha_1} \times \mathbb{Z}_4^{\alpha_2} \times \mathbb{Z}_8^{\alpha_3}$. A $\mathbb{Z}_2\mathbb{Z}_4\mathbb{Z}_8$-linear Hadamard code is a Hadamard…
The Kronecker family of the genetic matrices is investigated, which is based on the genetic matrix [C T; A G], where C, T, A, G are the letters of the genetic alphabet. The matrix [C T; A G] in the second Kronecker power is the (4*4)-matrix…
A closed formula multiallelic Walsh (or Hadamard) transform is introduced. Basic results are derived, and a statistical interpretation of some of the resulting linear forms is discussed.
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
A matrix-compression algorithm is derived from a novel isogenic block decomposition for square matrices. The resulting compression and inflation operations possess strong functorial and spectral-permanence properties. The basic observation…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the…
We introduce Graphical Algebraic Geometry (GAG), a family of diagrammatic languages extending the Graphical Linear Algebra programme. We construct several languages within this family and prove that they are universal and complete for the…