Non-Degenerate Graphical Representation of DNA Sequences and its Applications to Phylogenetic Analysis

Title:Non-Degenerate Graphical Representation of DNA Sequences and its Applications to Phylogenetic Analysis

Volume: 16 Issue: 8

Author(s): Yan Yang, Yingying Zhang, Meiduo Jia, Chun Li and Liangyu Meng

Affiliation:

Keywords: ALE-index, DNA, graphical representation, nondegeneracy, phylogenetic analysis.

Abstract: In this paper, we propose a new 3-D graphical representation of a DNA sequence and prove that it has two properties: (1) there is no circuit in the graph; (2) there exists a one-to-one correspondence between a DNA sequence and the graph. These properties guarantee it has nondegeneracy. Based on the 3-D graphical representation, we characterize a DNA sequence by a 12-dimensional vector whose components are normalized ALE-indexes of the corresponding L/L matrices. The proposed approach is tested by the phylogenetic analysis on three datasets, and the experimental assessment demonstrates its efficiency.

Cite this article as:

Yang Yan, Zhang Yingying, Jia Meiduo, Li Chun and Meng Liangyu, Non-Degenerate Graphical Representation of DNA Sequences and its Applications to Phylogenetic Analysis, Combinatorial Chemistry & High Throughput Screening 2013; 16 (8) . https://dx.doi.org/10.2174/1386207311316080001