Vector representation and its application of DNA sequences based on nucleotide triplet codons.

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Nucleotide triplets carry more biological and genetic information than single nucleotides.
• Existing methods for DNA sequence analysis have limitations in capturing comprehensive information.

Purpose of the Study:

• To propose a new 3D-vector representation method for DNA sequences.
• To enable numerical characterization for DNA sequence comparison and phylogenetic tree reconstruction.

Main Methods:

• Utilized molecular weight of nucleotide triplets to define a reference plane.
• Mapped DNA sequences into curves using 3D coordinate transformations and accumulation.
• Extracted eigenvalues from the D/D matrix for numerical characterization.

Main Results:

• Developed a novel 3D-vector representation for DNA sequences.
• Demonstrated the method's potential for describing, comparing, and analyzing DNA sequences.
• Showcased the application in phylogenetic tree reconstruction.

Conclusions:

• The proposed 3D-vector method offers a new perspective for biological sequence analysis.
• This technique provides a robust framework for comparative genomics and evolutionary studies.