New Algorithm for Determining the Similarities of Nucleotide Sequences Based on Comparisons of Torsion of Discrete Curves

Abstract

Discrete curves can be used to characterize sequences and the complete coding information of DNA in three-dimensional space. When the curve possesses properties that, in a mapping relationship, mirror those of DNA sequences, its characteristic values reveal the biological characteristics of a DNA sequence. By describing a DNA sequence using the recent Z curve model, we here propose a new method to judge the similarities of discrete DNA curves based on comparisons of the torsion of the curves. This comparative method was verified by quantitatively analyzing the similarities of cDNA sequences of 10 types of avian influenza viruses. Compared with a traditional dynamic programming algorithm, this new method takes full advantage of computer geometry for genetic comparative analyses by shifting from the traditional approach of a direct comparison of gene sequence characteristics to a comparison of the similarity of spatially discrete curves.