相关论文: A p-Adic Model of DNA Sequence and Genetic Code

Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…

For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…

The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…

We discuss the similarity of the degeneration structure of the genetic code with a pure number theoretic -- ``divisors code.'' The most interesting thing about our observation is not that there is a connection between number theory and the…

Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…

A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…

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…

In this short paper, it is shown that the multiplet structure of the standard genetic code is derivable from the total number of nucleotides contained in 64 codons, 192, a small number. The degeneracy class-number is derived as the number…

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,…

The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…

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…

This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…

Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…

How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…

By starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient subspaces of the…

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 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…