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image of Improved Visualization Method of DNA Sequences and its Application in Phylogenetic Analysis

Abstract

Introduction

With a large number of species' genomes assembled, sequence comparison has become an effective method for further studying biological classification and evolution. Traditional sequence alignment relies on predefined scoring functions, but it is computationally intensive and lacks molecular justification for scoring the differences between sequences. Therefore, we have developed a graphical representation method for DNA sequences to facilitate better sequence comparison and evolutionary analysis.

Method

In this article, we introduce a novel method for representing DNA sequences using three-dimensional (3D) graphics. This method possesses two significant properties: (1) the graphical representation is acyclic; (2) each DNA sequence maintains a bijective relationship with its graphical representation.

Result

Leveraging this proposed visualization method, we computed the corresponding ALE index for any DNA sequence by converting it into an matrix and constructed a 12-dimensional feature vector. The feasibility of our proposed method has been validated through the construction of phylogenetic trees in four test sets: terrestrial vertebrates, hantavirus, fish and Japanese encephalitis virus.

Discussion

This method enables both quantitative analysis and visual comparison of DNA sequences, providing a versatile tool for evolutionary studies.

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2025-07-01
2025-10-30

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Improved Visualization Method of DNA Sequences and its Application in Phylogenetic Analysis
Bentham Science Publishers ; https://doi.org/10.2174/0113862073379972250612103433
/content/journals/cchts/10.2174/0113862073379972250612103433
/content/journals/cchts/10.2174/0113862073379972250612103433
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  • Article Type:     Research Article
Keywords: phylogenetic analysis ; L/L matrix ; virus ; nondegeneracy ; graphical representation ; ALE-index ; DNA

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