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

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

Journal Name: Combinatorial Chemistry & High Throughput Screening
Accelerated Technologies for Biotechnology, Bioassays, Medicinal Chemistry and Natural Products Research

Volume 16 , Issue 8 , 2013

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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.

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

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Article Details

VOLUME: 16
ISSUE: 8
Year: 2013
Published on: 31 July, 2013
Page: [585 - 589]
Pages: 5
DOI: 10.2174/1386207311316080001
Price: $65

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