Visualization and comparison of DNA sequences by use of three-dimensional trajectories

Abstract

In this paper, we propose a visualization tool for dexoyribonucleic acid (DNA) sequences by the use of three-dimensional (3-D) trajectories (TDT). In the proposed method, four different nucleotides are assigned by four corresponding positions in the 3-D space, which are equally spaced and the origin is the centroid of four positions. With the distance accumulated from the distances between multiple consecutive two positions, a DNA sequence can be represented by a trajectory in the 3-D space. A global view of the DNA sequence can thus be obtained no matter how large the sequence is. The alignment of two DNA sequences can be determined by the use of correlation operation on the trajectories. From our simulation results, the TDTs for different functions of DNA sequences vary a lot and thus are easy to be distinguished. On the other hand, there exist some similarities between the trajectories for the same type of DNA sequences obtained from different kinds of creatures. Therefore, in addition to the low computation complexity, the proposed visualization tool can easily discriminate the differences and similarities among various DNA sequences.