Related papers: A p-Adic Model of DNA Sequence and Genetic Code
The standard genetic code multiplet structure as well as the correct degeneracies, class by class, are all extracted from the (unique) number 23, the order of the permutation group of 23 objects.
The algebraic structures of the genetic code are most important to obtain additional information about the semantic code and its applications. In this paper we define two dual Boolean codon lattices of the genetic code using hydrogen bond…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic…
In the present work, 16 genetic code doublets and their cognate amino acids in the genetic code are fitted into a polyhedron model. Based on the structural regularity in nucleobases, and by using a series of common-sense topological…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
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 genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
The biological distinction between the base positions in the codon, the chemical types of bases (purine and pyrimidine) and their hydrogen bond number have been the most relevant codon properties used in the genetic code analysis. Now,…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
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…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…