Defragged Binary I Ching Genetic Code Chromosomes Compared to Nirenberg's and Transformed into Rotating 2D Circles and Squares and into a 3D 100% Symmetrical Tetrahedron Coupled to a Functional One to Discern Start From Non-Start Methionines through a Stella Octangula

Comparative study of encoded and alignment-based methods for virus taxonomy classification

The emergence of viruses and their variants has made virus taxonomy more important than ever before in controlling the spread of diseases. The creation of efficient treatments and cures that target particular virus properties can be aided by understanding virus taxonomy. Alignment-based methods are commonly used for this task, but are computationally expensive and time-consuming, especially when dealing with large datasets or when detecting new virus variants is time sensitive. An alternative approach, the encoded method, has been developed that does not require prior sequence alignment and provides faster results. However, each encoded method has its own claimed accuracy. Therefore, careful evaluation and comparison of the performance of different encoded methods are essential to identify the most accurate and reliable approach for virus taxonomy classification. This study aims to address this issue by providing a comprehensive and comparative analysis of the potential of encoded methods for virus classification and phylogenetics. We compared the vectors generated for each encoded method using distance metrics to determine their similarity to alignment-based methods. The results and their validation show that K-merNV followed by CgrDft encoded methods, perform similarly to state-of-the-art multi-sequence alignment methods. This is the first study to incorporate and compare encoded methods that will facilitate future research in making more informed decisions regarding selection of a suitable method for virus taxonomy.

Effective Encoding for DNA Sequence Visualization Based on Nucleotide's Ring Structure

Effective representation of DNA sequences is one of the important tasks in the study of genome sequences. In this paper, we propose a graphical representation of DNA sequences based on nucleotide ring structure. In the proposed representation, we convert DNA sequences into 16 dinucleotides on the surface of the hexagon so that it can preserve nucleotide's chemical property and positional information. Our approach can provide capability of efficient similarity comparison between DNA sequences and also high comparison accuracy. Furthermore, our approach satisfies uniqueness and no degeneracy of DNA sequences. In the experimental study, we use phylogeny analysis for evolutionary relationship among different species. Extensive performance study shows that the proposed method can give better performance than existing methods in comparison with the degree of similarity.