Related papers: p-Adic Degeneracy of the Genetic Code
The degeneracy of central configurations in the planar $N$-body problem makes their enumeration problem hard and the related dynamics appealing. To truly understand the bifurcations of central configurations, we should work in the FULL…
Predictive coding (PC) networks are a biologically interesting class of neural networks. Their layered hierarchy mimics the reciprocal connectivity pattern observed in the mammalian cortex, and they can be trained using local learning rules…
What could cause the emergence of non-encoding codons in the course of evolution of the genetic code? Hypothesis of evolution of the genetic code from GC to the AGUC-alphabet account for existence of stop codons.
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
The multidimensional convolutional codes are an extension of the notion of convolutional codes (CCs) to several dimensions of time. This paper explores the class of two-dimensional convolutional codes (2D CCs) and 2D tail-biting…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
Part 1 of the study intends to show that the universal trend of amino acid gain and loss discovered by Jordan et al. (2005) can be accounted for by the spontaneity of DNA typical damages. These damages lead to replacements of guanine and…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Decoding of convolutional codes poses a significant challenge for coding theory. Classical methods, based on e.g. Viterbi decoding, suffer from being computationally expensive and are restricted therefore to codes of small complexity. Based…
In this paper, we develop the theory for constructing DNA cyclic codes of odd length over $R=\Z_4[u]/\langle u^2-1 \rangle$ based on the deletion distance. Firstly, we relate DNA pairs with a special 16 elements of ring $R$. Cyclic codes of…
Generalized quasi-cyclic (GQC) codes form a natural generalization of quasi-cyclic (QC) codes. They are viewed here as mixed alphabet codes over a family of ring alphabets. Decomposing these rings into local rings by the Chinese Remainder…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…
Protein variant libraries produced by site-directed mutagenesis are a useful tool utilized by protein engineers to explore variants with potentially improved properties, such as activity and stability. These libraries are commonly built by…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
The Z_64-algebra of the genetic code and DNA sequences of length N was recently stated. In order to beat the limits of this structure such as the impossibility of non-coding region analysis in genomes and the impossibility of the insertions…
The key to a robust and efficient implementation of a computational geometry algorithm is an efficient algorithm for detecting degenerate predicates. We study degeneracy detection in constructing the free space of a polyhedron that rotates…