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

Li Dong1, Xinyang Jiang2, Yong Liu3

  • 1The College of Health Humanities, Jinzhou Medical University, Jinzhou 121001, China.

Combinatorial Chemistry & High Throughput Screening
|July 3, 2025
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Summary

This study introduces a novel 3D graphical method for DNA sequence comparison, offering a computationally efficient and molecularly justified alternative to traditional alignment for evolutionary analysis.

Keywords:
ALE-indexDNAgraphical representationnondegeneracyphylogenetic analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genome assembly has increased the need for effective DNA sequence comparison.
  • Traditional sequence alignment methods are computationally intensive and lack molecular basis for scoring differences.
  • A new graphical representation method for DNA sequences is proposed to address these limitations.

Purpose of the Study:

  • To develop a novel graphical representation for DNA sequences.
  • To facilitate improved sequence comparison and evolutionary analysis.
  • To provide a method with molecular justification for scoring sequence differences.

Main Methods:

  • Representing DNA sequences using three-dimensional (3D) graphics.
  • Ensuring the graphical representation is acyclic.
  • Maintaining a bijective relationship between DNA sequences and their graphical representations.

Main Results:

  • Computed the ALE index for DNA sequences via L/L matrix conversion.
  • Constructed a 12-dimensional feature vector for each sequence.
  • Demonstrated the method's utility in phylogenetic tree construction.

Conclusions:

  • The proposed 3D graphical method is feasible for DNA sequence comparison.
  • Validated through phylogenetic tree construction in diverse datasets (vertebrates, hantavirus, fish, viruses).
  • Offers a promising approach for evolutionary and classification studies.