Code Table Research Articles

Maximal Genetic Code Symmetry Is a Physicochemical Purine-Pyrimidine Symmetry Language for Transcription and Translation in the Flow of Genetic Information from DNA to Proteins.

Until now, research has not taken into consideration the physicochemical purine-pyrimidine symmetries of the genetic code in the transcription and translation processes of proteinogenesis. Our Supersymmetry Genetic Code table, developed in 2022, is common and unique for all RNA and DNA living species. Its basic structure is a purine-pyrimidine symmetry net with double mirror symmetry. Accordingly, the symmetry of the genetic code directly shows its organisation based on the principle of nucleotide Watson-Crick and codon-anticodon pairing. The maximal purine-pyrimidine symmetries of codons show that each codon has a strictly defined and unchangeable position within the genetic code. We discovered that the physicochemical symmetries of the genetic code play a fundamental role in recognising and differentiating codons from mRNA and the anticodon tRNA and aminoacyl-tRNA synthetases in the transcription and translation processes. These symmetries also support the wobble hypothesis with non-Watson-Crick pairing interactions between the translation process from mRNA to tRNA. The Supersymmetry Genetic Code table shows a specific arrangement of the second base of codons, according to which it is possible that an anticodon from tRNA recognises whether a codon from mRNA belongs to an amino acid with two or four codons, which is very important in the purposeful use of the wobble pairing process. Therefore, we show that canonical and wobble pairings essentially do not lead to misreading and errors during translation, and we point out the role of physicochemical purine-pyrimidine symmetries in decreasing disorder according to error minimisation and preserving the integrity of biological processes during proteinogenesis.

On Recursive Tiling of some Mathematical Objects.

This essay, in a novel way, uses various tiles, such as dominoes, square-, interlocking-, and flow-tiles, to visualize approximations to recursively defined, potentially infinite mathematical objects, such as binary code tables, and variants of the space-filling Hilbert curve. The power of L-systems is shown by defining these tiled objects as L-systems.

A tRNA modification pattern that facilitates interpretation of the genetic code.

Interpretation of the genetic code from triplets of nucleotides to amino acids is fundamental to life. This interpretation is achieved by cellular tRNAs, each reading a triplet codon through its complementary anticodon (positions 34-36) while delivering the amino acid charged to its 3'-end. This amino acid is then incorporated into the growing polypeptide chain during protein synthesis on the ribosome. The quality and versatility of the interpretation is ensured not only by the codon-anticodon pairing, but also by the post-transcriptional modifications at positions 34 and 37 of each tRNA, corresponding to the wobble nucleotide at the first position of the anticodon and the nucleotide on the 3'-side of the anticodon, respectively. How each codon is read by the matching anticodon, and which modifications are required, cannot be readily predicted from the codon-anticodon pairing alone. Here we provide an easily accessible modification pattern that is integrated into the genetic code table. We focus on the Gram-negative bacterium Escherichia coli as a model, which is one of the few organisms whose entire set of tRNA modifications and modification genes is identified and mapped. This work provides an important reference tool that will facilitate research in protein synthesis, which is at the core of the cellular life.

Optimal Quaternary Hermitian LCD Codes.

Linear complementary dual (LCD) codes, which are a class of linear codes introduced by Massey, have been extensively studied in the literature recently. It has been shown that LCD codes play a role in measures to counter passive and active side-channel analyses on embedded cryptosystems. In this paper, tables are presented of good quaternary Hermitian LCD codes and they are used in the construction of puncturing, shortening and combination codes. The results of this, including three tables of the best-known quaternary Hermitian LCD codes of any length n≤25 with corresponding dimension k, are presented. In addition, many of these quaternary Hermitian LCD codes given in this paper are optimal and saturate the lower or upper bound of Grassl's code table, and some of them are nearly optimal.

Theories of the origin of the genetic code: Strong corroboration for the coevolution theory

I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons and that of amino acids. Instead, the intervention of natural selection in organizing the genetic code would appear to be highly compatible with the main mechanism of structuring the genetic code as supported by the coevolution theory. This would make the coevolution theory the only plausible explanation for the origin of the genetic code.

An Encoding Table Corresponding to ASCII Codes for DNA Data Storage and a New Error Correction Method HMSA.

DNA storage stands out from other storage media due to its high capacity, eco-friendliness, long lifespan, high stability, low energy consumption, and low data maintenance costs. To standardize the DNA encoding system, maintain consistency in character representation and transmission, and link binary, base, and character together, this paper combines the encoding method with ASCII code to construct an ASCII-DNA encoding table. The encoding method can encode not only pure text information but also audio and video information and satisfies the GC content constraint and the homopolymer constraint, with the encoding density reaching 1.4 bits/nt. In particular, when encoding textual information, it directly skips the binary conversion process, which reduces the complexity of encoding, and increasing the encoding density to 1.6 bits/nt. In order to solve the problem of errors in sequences, under the influence of heuristic algorithms, this paper proposes a new error correction method (HMSA) by combining minimum Hamming distance, multiple sequence alignment, and encoding scheme. It can correct not only substitution, insertion, and deletion errors in Reads but also consecutive errors in Reads. It greatly improves the utilization of the Reads and avoids the waste of resources. Simulation results show that the recovery rate of Reads increases with the increasing number of sequencing times. When the number of erroneous bases in a 150nt sequence reaches 5nt, the error correction rate can exceed 96% by sequencing the base sequence only 10 times regardless of whether the errors are consecutive or not. Additionally, the HMSA error correction method is applicable to all coding schemes for lookup code table types.

Optimization and Performance Analysis of CAT Method for DNA Sequence Similarity Searching and Alignment.

Bioinformatics is a rapidly developing field enabling scientific experiments via computer models and simulations. In recent years, there has been an extraordinary growth in biological databases. Therefore, it is extremely important to propose effective methods and algorithms for the fast and accurate processing of biological data. Sequence comparisons are the best way to investigate and understand the biological functions and evolutionary relationships between genes on the basis of the alignment of two or more DNA sequences in order to maximize the identity level and degree of similarity. This paper presents a new version of the pairwise DNA sequences alignment algorithm, based on a new method called CAT, where a dependency with a previous match and the closest neighbor are taken into consideration to increase the uniqueness of the CAT profile and to reduce possible collisions, i.e., two or more sequence with the same CAT profiles. This makes the proposed algorithm suitable for finding the exact match of a concrete DNA sequence in a large set of DNA data faster. In order to enable the usage of the profiles as sequence metadata, CAT profiles are generated once prior to data uploading to the database. The proposed algorithm consists of two main stages: CAT profile calculation depending on the chosen benchmark sequences and sequence comparison by using the calculated CAT profiles. Improvements in the generation of the CAT profiles are detailed and described in this paper. Block schemes, pseudo code tables, and figures were updated according to the proposed new version and experimental results. Experiments were carried out using the new version of the CAT method for DNA sequence alignment and different datasets. New experimental results regarding collisions, speed, and efficiency of the suggested new implementation are presented. Experiments related to the performance comparison with Needleman-Wunsch were re-executed with the new version of the algorithm to confirm that we have the same performance. A performance analysis of the proposed algorithm based on the CAT method against the Knuth-Morris-Pratt algorithm, which has a complexity of O(n) and is widely used for biological data searching, was performed. The impact of prior matching dependencies on uniqueness for generated CAT profiles is investigated. The experimental results from sequence alignment demonstrate that the proposed CAT method-based algorithm exhibits minimal deviation, which can be deemed negligible if such deviation is considered permissible in favor of enhanced performance. It should be noted that the performance of the CAT algorithm in terms of execution time remains stable, unaffected by the length of the analyzed sequences. Hence, the primary benefit of the suggested approach lies in its rapid processing capabilities in large-scale sequence alignment, a task that traditional exact algorithms would require significantly more time to perform.

ПРИКЛАДНАЯ ЛИНГВИСТИКА В ОРДЕНА ЗНАК ПОЧЕТА ИНСТИТУТЕ ИСТОРИИ, ЯЗЫКА И ЛИТЕРАТУРЫ УФИЦ РАН: ОСНОВНЫЕ ВЕХИ

The article analyzes the development of applied linguistics within the framework of Bashkir linguistics, as well as the formation of this field. Most researchers working in the field of applied linguistics consider it to be a multidisciplinary field that encompasses all existing research. However, there is still no clear definition of what constitutes this term. In the article, applied linguistics is defined as referring to areas that involve the use of mathematical methods, computer-aided text processing, and the creation and analysis of linguistic databases. These areas have been active fields of research at the Institute of History, Language and Literature of the Ufa Federal Research Center of the Russian Academy of Sciences for over 30 years. The first steps towards this goal in the Bashkir linguistics were taken by the group “Automation of Lexicography”, which was founded in 1991. During its 11-year existence, the team developed frequency dictionaries for the language in the works of classical Bashkir literature by D. Yulty, as well as frequency dictionaries on different styles of Bashkir, primary school textbooks, and other materials. Due to the widespread adoption of computer technologies, which required the creation of standards for software, localization, support for operating systems, and promotion of the Bashkir language online, a laboratory for linguistics and information technology has been established on the basis of this group. The laboratory successfully completed these tasks: they presented standards for keyboard layouts and code tables; they participated in the localization of Lexicon, FineReader, Mozilla, Disco Commander and Chameleon programs; and they created national fonts and implemented language support for Windows and Linux operating systems. These works were the foundation for the full functionality of the language in the digital world. On their basis, the laboratory developed a terminological database operating on the internet, an information system for the Machine Fund of the Bashkir language, and corpus projects on prose, journalist and folklore texts in the Bashkir language. Based on these latter projects, certain issues regarding the syntactic structures of proverbs and sayings in the national language have been investigated. In order to continue dialectological research and to create a database of dialects of the national language, the laboratory was transformed into the Department of Applied Linguistics and Dialectology in 2022. Today, the department continues to work on corpus projects of the Bashkir language and collects expedition materials for a geographic information database on regional dialects. Based on these materials, a great deal of scientific work is carried out to clarify problems of the function of oral Bashkir speech within the media, as well as to determine phonetic and lexico-grammatical characteristics of the Northwest dialect.

Toward Generalizable Machine Learning Models in Speech, Language, and Hearing Sciences: Estimating Sample Size and Reducing Overfitting.

Many studies using machine learning (ML) in speech, language, and hearing sciences rely upon cross-validations with single data splitting. This study's first purpose is to provide quantitative evidence that would incentivize researchers to instead use the more robust data splitting method of nested k-fold cross-validation. The second purpose is to present methods and MATLAB code to perform power analysis for ML-based analysis during the design of a study. First, the significant impact of different cross-validations on ML outcomes was demonstrated using real-world clinical data. Then, Monte Carlo simulations were used to quantify the interactions among the employed cross-validation method, the discriminative power of features, the dimensionality of the feature space, the dimensionality of the model, and the sample size. Four different cross-validation methods (single holdout, 10-fold, train-validation-test, and nested 10-fold) were compared based on the statistical power and confidence of the resulting ML models. Distributions of the null and alternative hypotheses were used to determine the minimum required sample size for obtaining a statistically significant outcome (5% significance) with 80% power. Statistical confidence of the model was defined as the probability of correct features being selected for inclusion in the final model. ML models generated based on the single holdout method had very low statistical power and confidence, leading to overestimation of classification accuracy. Conversely, the nested 10-fold cross-validation method resulted in the highest statistical confidence and power while also providing an unbiased estimate of accuracy. The required sample size using the single holdout method could be 50% higher than what would be needed if nested k-fold cross-validation were used. Statistical confidence in the model based on nested k-fold cross-validation was as much as four times higher than the confidence obtained with the single holdout-based model. A computational model, MATLAB code, and lookup tables are provided to assist researchers with estimating the minimum sample size needed during study design. The adoption of nested k-fold cross-validation is critical for unbiased and robust ML studies in the speech, language, and hearing sciences. https://doi.org/10.23641/asha.25237045.

The Supersymmetry Genetic Code Table and Quadruplet Symmetries of DNA Molecules Are Unchangeable and Synchronized with Codon-Free Energy Mapping during Evolution.

The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: (1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)] and (2) of bases in the form of codons; (3) direct-complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns; (4) A + T-rich and C + G-rich alternate codons in the same row between both columns of the genetic code; (5) the same position between divided and undivided codon boxes in relation to horizontal mirror symmetry axis. The SSyGC table has a unique physicochemical purine-pyrimidine symmetry net which is as the core symmetry common for all, with more than thirty different nuclear and mitochondrial genetic codes. This net is present in the SSyGC table of all RNA and DNA living species. None of these symmetries are present in the Standard Genetic Code (SGC) table which is constructed on the alphabetic horizontal and vertical U-C-A-G order of bases. Here, we show that the free energy value of each codon incorporated as fundamentally mapping the "energy code" in the SSyGC table is compatible with mirror symmetry. On the other hand, in the SGC table, the same free energy values of codons are dispersed and a mirror symmetry between them is not recognizable. At the same time, the mirror symmetry of the SSyGC table and the DNA quadruplets together with our classification of codons/trinucleotides are perfectly imbedded in the mirror symmetry energy mapping of codons/trinucleotides and point out in favor of maintaining the integrity of the genetic code and DNA genome. We also argue that physicochemical symmetries of the SSyGC table in the manner of the purine-pyrimidine symmetry net, the quadruplet symmetry of DNA molecule, and the free energy of codons have remined unchanged during all of evolution. The unchangeable and universal symmetry properties of the genetic code, DNA molecules, and the energy code are decreasing disorder between codons/trinucleotides and shed a new light on evolution. Diversity in all living species on Earth is broad, but the symmetries of the Supersymmetry Genetic Code as the code of life and the DNA quadruplets related to the "energy code" are unique, unchangeable, and have the power of natural laws.

Electron Oscillation-Induced Splitting Electroluminescence from Nano-LEDsfor Device-Level Encryption.

Data security is a major concern in digital age, which generally relies on algorithm-based mathematical encryption. Recently, encryption techniques based on physical principles are emerging and being developed, leading to the new generation of encryption moving from mathematics to the intersection of mathematics and physics. Here, device-level encryption with ideal security is ingeniously achieved using modulation of the electron-hole radiative recombination in a GaN-light-emitting diode (LED). When a nano-LED is driven in the non-carrier injection mode, the oscillation of confined electrons can split what should be a single light pulse into multiple pulses. The morphology (amplitude, shape, and pulse number) of those history-dependent multiple pulses that act as carriers for transmitted digital information depends highly on the parameters of the driving signals, which makes those signals mathematically uncrackable and can increase the volume and security of transmitted information. Moreover, a hardware and software platform are designed to demonstrate the encrypted data transmission based on the device-level encryption method, enabling recognition of the entire ASCII code table. The device-level encryption based on splitting electroluminescence provides an encryption method during the conversion process of digital signals to optical signals and can improve the security of LED-based communication.

Towards Chinese text and DNA shift encoding scheme based on biomass plasmid storage.

DNA, as the storage medium in organisms, can address the shortcomings of existing electromagnetic storage media, such as low information density, high maintenance power consumption, and short storage time. Current research on DNA storage mainly focuses on designing corresponding encoders to convert binary data into DNA base data that meets biological constraints. We have created a new Chinese character code table that enables exceptionally high information storage density for storing Chinese characters (compared to traditional UTF-8 encoding). To meet biological constraints, we have devised a DNA shift coding scheme with low algorithmic complexity, which can encode any strand of DNA even has excessively long homopolymer. The designed DNA sequence will be stored in a double-stranded plasmid of 744bp, ensuring high reliability during storage. Additionally, the plasmid's resistance to environmental interference ensuring long-term stable information storage. Moreover, it can be replicated at a lower cost.

Three Pass Protocol for Key Security Using Affine Cipher Algortima and Exclusive-or (Xor) Combination

Information is a very important concern in today's technological era, especially in terms of security through the exchange of information that is so fast that people can easily get various kinds of information. Information obtained easily through recording or openly disseminating data, XOR Cipher is an algorithm used to secure messages and texts but has weaknesses due to simple computation, therefore to strengthen security in XOR Cipher communication protocols can be added to secure key exchange on XOR Ciphers. Affine Cipher can be combined with Exclusive-OR (XOR) for text message security. Through the Affine Cipher algorithm with Key can change the unknown Plaintext, so that the Plaintext is kept secret. The Exclusive-OR (XOR) combination by changing each Character in each Plaintext according to the ASCII Code table can shorten the Key encoding process, so that Plaintext remains safe to send. The Affine Cipher Algorithm and the Exclusive-OR (XOR) Combination for Plaintext security levels are better because the Plaintext encryption and decryption processes are carried out twice with different cryptographic algorithms.

Current Status of Quang Ninh Tourism Promotion in Electronic Newspaper and Some Policy Implications (Survey of Quang Ninh Electronic Newspapers, Tien Phong, Labor, Youth)

Newspapers in general, and electronic newspapers in particular, play an indirect role as a "push" for the continuous development of Vietnamese tourism. During the COVID-19 pandemic recovery era, electronic newspapers are an important channel for the tourism industry to promote information and tourism services, as well as position the industry. How have electronic newspapers contributed to tourism promotion? From June 2022 to June 2023, a survey was conducted with 455 news articles from four electronic newspapers: Quang Ninh, Tien Phong, Lao Dong, and Thanh Nien, using the quantitative method of analyzing newspaper content with an analysis code table to answer the above research question within the scope of tourism promotion in Quang Ninh province. From the survey results, the authors initially identified the current situation and proposed solutions to improve the quality of advertising on electronic newspapers because Quang Ninh has such rich tourism resources, unique potential, and outstanding opportunities to develop all types of tourism, contributing to the overall growth of the tourism industry.

New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group

Phylogenetics is the study of ancestral relationships among biological species. Such sequence analyses are often represented as phylogenetic trees. The branching pattern of each tree and its topology reflect the evolutionary relatedness between analyzed sequences. We present a Klein four-group algorithm (K4A) for the evolutionary analysis of nucleotide and amino acid sequences. Klein four-group set of operators consists of: identity e (U), and three elements—a = transition (C), b = transversion (G) and c = transition-transversion or complementarity (A). We generated Klein four-group based distance matrices of: 1. Cayley table (CK4), 2. Table rows (K4R), 3. Table columns (K4C), and 4. Euclidean 2D distance (K4E). The performance of the matrices was tested on a dataset of RecA proteins in bacteria, eukaryotes (Rad51 homolog) and archaea (RadA homolog). RecA and its functional homologs are found in all species, and are essential for the repair and maintenance of DNA. Consequently, they represent a good model for the study of evolutionary relationship of protein and nucleotide sequences. The ancestral relationship between the sequences was correctly classified by all K4A matrices concerning general topology. All distance matrices exhibited small variations among species, and overall results of tree classification were in agreement with the general patterns obtained by standard BLOSUM and PAM substitution matrices. During the evolution of a code there is a phase of optimization of system rules, the ambiguity of a code is eliminated, and the system starts producing specific components. Klein four-group algorithm is consistent with the concept of ambiguity reduction. It also enables the use of different genetic code table variants optimized for particular transitions in evolution based on biological specificity.

Online Resources: Coding for Vaccine and Immunization Administration Services

The costs of providing immunization services in a pediatric practice are not insignificant. It is important to use business and coding practices that protect a practice’s investment in these services. This article reviews American Academy of Pediatrics (AAP) online resources to assist members with financing and payment to support in-office immunization services. Among those resources are AAP vaccine financing and payment support resources AAP Vaccine Coding Table Assistance with vaccine payment issues

The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code.

Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson-Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons' relationship as to how to develop the DNA molecule on the principle of Watson-Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system.

A novel coal-gangue recognition method in underground coal mine based on image processing

ABSTRACT This study proposes a coal-gangue recognition method based on Retinex and extreme learning machine. The traditional Retinex has many limitations, including halo artifacts, excessive enhancement, and noise amplification in dark areas. To handle these, first, a modified multi-scale Retinex image enhancement algorithm based on hue, saturation, value color space, and bidimensional empirical mode decomposition named modified multi-scale Retinex algorithm with color restoration (MMSRCR) is proposed herein. On-site images are used to verify the effectiveness of the MMSRCR. Second, a preliminary segmentation method for coal-gangue images based on the optimal entropy threshold optimized by the improved quantum genetic algorithm is designed. The proposed segmentation method performs excellent stability compared with other traditional methods. Third, the adhesion part of the ore is further segmented based on the morphology opening operation and watershed algorithm. Then, the feature space of each enclosed area is extracted using the chain code and line segment tables. The improved extreme learning machine completes the classification of these areas, and the coal-gangue visual ratio recognition method is proposed. Finally, an experimental platform for visual ratio recognition is built to verify the proposed method. The experimental results show that the proposed method can accurately identify the visual ratio of coal-gangue.

Investigation of codon alternation patterns in two neurodegenerative diseases through numerical representation and codon classification

Several evidences claim similarities between two neuro-degenerative diseases viz.Parkinson's disease and Glaucoma. But proper pathogenetic factors specially in bio-molecular level are still not cleared. Hence, the prime objectives of the study here is to investigate evolutionary relationships among the genes involved in the diseases and to understand the pattern of mutations responsible in the two disease pathogenesis. Reported research work established that the strengths of nucleotides (according to number of hydrogen bonds they have) have a deep impact on protein formation. Moreover, depending upon the position the virulence of mutation differs. Effective mutation analysis can help to predict the fate of the diseased individual which can be validated later by in-vitro experiments. In this present study, PARKIN, PINK1, and DJ1 genes are taken for Parkinson's disease and CYP1B1 and MYOC for Glaucoma. Importance has been given to the nucleotides existing at first and second positions of a codon. We followed Rumer's classification of doublets based on the strength of nucleotides and Duplij’s numeric interpretation of the strength of each nucleotide as “determinative degree” to classify the 64 codons and corresponding amino acids into three major classes viz. strong, transitional, and weak. The determinative degrees of all 64 codons and corresponding 20 amino acids are calculated to define their strengths. The complete analysis is carried out based on this classification scheme. Further we proposed an alignment-free method SSADDA (Sequence Similarity Analysis using Determinative Degree of Amino acid) based on determinative degree of amino acid and applied to the wild type amino acid sequences to measure proximity among themselves. The methodology gives us a more microscopic view of the existing genetic code table.

Hanchu Huang

Graphical Abstract „The next big goal of my research is to explore more efficient strategies for the ring-opening polymerization of macrocyclic monomers … I am waiting for the day when someone will discover a new code table beyond the periodic table, bringing us to think about the chemical world in a different way.“ Find out more about Hanchu Huang in his Introducing … Profile.