Codons and codes
نویسندگان
چکیده
In this paper we assemble a few ingredients that are remotely connected to each other, but governed by the rule of coding theory ([1], [12]) and formal language theory, i.e. cyclic codes and DNA codes. Our interest arose from the remark that there exist both linear and circular DNAs in higher living organisms. We state the theory of codes in a wide sense due to [1] in order to understand the circular DNAs while we state rudiments of formal language theory as a means to interpret genes. We hope this will be a starter for unifying two approaches depending on the theory of codes and that of formal language.
منابع مشابه
Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum
mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not m...
متن کاملOn the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes
Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises al...
متن کاملGraph Theory Patterns in the Genetic Codes
The genetic code in biology describes how genes that are composed of DNA are translated into proteins composed of amino acids. There are twelve known genetic codes, the standard code used by most organisms, and alternate codes used by mitochondria and some lower organisms. These genetic codes can be represented as graphs, with vertices labeled by the amino acids and lines representing complemen...
متن کاملNon-Standard Genetic Codes Define New Concepts for Protein Engineering
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondri...
متن کاملSeveral remarks on the metric space of genetic codes
A genetic code, the mapping from trinucleotide codons to amino acids, can be viewed as a partition on the set of 64 codons. A small set of non-standard genetic codes is known, and these codes can be mathematically compared by their partitions of the codon set. To measure distances between set partitions, this study defines a parameterised family of metric functions that includes Shannon entropy...
متن کاملGenetic Code Population Dynamics in a Simulated System of Protocells
An evolutionary algorithm was developed to investigate how the biological genetic code may have evolved. Graph theoretical "degree sequences" were derived from the simulated genetic codes of "organisms" produced by this algorithm. These graph theory metrics were used as a measure of similarity among evolving genetic codes, in order to classify the set of organisms into equivalence classes witho...
متن کامل