Related papers: The genetic code multiplet structure, in one numbe…
A unique decoding algorithm for general AG codes, namely multipoint evaluation codes on algebraic curves, is presented. It is a natural generalization of the previous decoding algorithm which was only for one-point AG codes. As such, it…
The number of atoms in the four ribonucleotides uridine monophosphate, cytidine monophosphate, adenine monophosphate and guanine monophosphate is taken as a key parameter. A mathematical relation describing the condensation of the three…
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
Permutation codes are a class of structured vector quantizers with a computationally-simple encoding procedure based on sorting the scalar components. Using a codebook comprising several permutation codes as subcodes preserves the…
Defant, Engen, and Miller defined a permutation to be uniquely sorted if it has exactly one preimage under West's stack-sorting map. We enumerate classes of uniquely sorted permutations that avoid a pattern of length three and a pattern of…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
For a given permutation or set partition there is a natural way to assign a genus. Counting all permutations or partitions of a fixed genus according to cycle lengths or block sizes, respectively, is the main content of this article. After…
Algebraic properties of the genetic code are analyzed. The investigations of the genetic code on the basis of matrix approaches ("matrix genetics") are described. The degeneracy of the vertebrate mitochondria genetic code is reflected in…
We introduce the simple parametrization for the space of codons (triples of nucleotides) by 8\times 8 table. This table (which we call the dyadic plane) possesses the natural 2-adic ultrametric. We show that after this parametrization the…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
This work aims at showing the relevance and the applications possibilities of the Fibonacci sequence, and also its q-deformed or quantum extension, in the study of the genetic code(s). First, after the presentation of a new formula, an…
A set of linearly constrained permutation matrices are proposed for constructing a class of permutation codes. Making use of linear constraints imposed on the permutation matrices, we can formulate a minimum Euclidian distance decoding…
We describe some configurations of conjugate permutations which may be used as a mathematical model of some genetical processes and crystal growth.
A combinatorial Gray code for a set of combinatorial objects is a sequence of all combinatorial objects in the set so that each object is derived from the preceding object by changing a small part. In this paper we design a Gray code for…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
In this article we consider square permutations, a natural subclass of permutations defined in terms of geometric conditions, that can also be described in terms of pattern avoiding permutations, and convex permutoninoes, a related subclass…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…