Related papers: The genetic code invariance: when Euler and Fibona…
An amino acid sequence of a protein may be decomposed into consecutive overlapping strings of length K. How unique is the converse, i.e., reconstruction of amino acid sequences using the set of K-strings obtained in the decomposition? This…
We construct an encoding of finite strings over a fixed finite alphabet as natural numbers, based on a block partition of the Fibonacci sequence. Each position in the string selects one Fibonacci number from a dedicated block, with unused…
Each linear code can be described by a code ideal given as the sum of a toric ideal and a non-prime ideal. In this way, several concepts from the theory of toric ideals can be translated into the setting of code ideals. It will be shown…
The study is aimed at revealing the most important substructures (fragments) of polyenes with heteroatoms determining the alteration in the conjugation energy of the whole compound due to substitution and the relevant charge redistribution.…
The generalized Fibonacci recurrence $g_n=g_{n-k}+g_{n-m}$ was recently used to demonstrate the theoretically optimal nature of limited senescence in morphologically symmetrically dividing bacteria. Here, we study this recurrence from a…
The idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…
Information is often encoded as an aperiodic chain of building blocks. Modern digital computers use bits as the building blocks, but in general the choice of building blocks depends on the nature of the information to be encoded. What are…
A motivation for studying the following problems comes from applications to Biology; see \cite{cifuentes20233d}. In the $3$-dimensional Euclidean space ${\bf{E}}^3$, fix six pairwise distinct points \begin{equation*} \label{eqA}…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
New analyses of the organization of the genetic code system together with their relation to the two classes of aminoacyl-tRNA synthetases are reported in this work. A closer inspection revealed how the enzymes and the 20 amino acids of the…
Unsupervised learning on high-dimensional RNA-seq data can reveal molecular subtypes beyond standard labels. We combine an autoencoder-based representation with clustering and stability analysis to search for rare but reproducible genomic…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been…
Ribonucleic acid (RNA) plays fundamental roles in biological systems, from carrying genetic information to performing enzymatic function. Understanding and designing RNA can enable novel therapeutic application and biotechnological…