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

Abstract Compared with single nucleotide, nucleotide triplet appears to contain more biological and genetic information, so it has been applied widely. We propose a new 3D-vector representation method of DNA sequences, namely use molecular weight of nucleotide triplet to define the ‘0’ molecular plane, then make the 3-D coordinate transformation to map a DNA sequence into a curve by the coordinate accumulation, and then extract the D/D matrix’s eigenvalues to describe, compare and analyze the DNA sequences as the numerical characterization. It is a new idea for comparison and phylogenetic trees’ reconstruction of biological sequences.