Related papers: Did Sequence Dependent Geometry Influence the Evol…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Codes have been used for centuries to convey secret information.To a cryptanalyst, the interception of a code is only the first step in recovering a secret message.Deoxyribonucleic acid (DNA) is a biological and molecular code.Through the…
All known life forms are based upon a hierarchy of interwoven feedback loops, operating over a cascade of space, time and energy scales. Among the most basic loops are those connecting DNA and proteins. For example, in genetic networks, DNA…
Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be interested in these molecules? As we will see, DNA is an…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
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…
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…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
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…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
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…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…