alexa Non-degenerate graphical representation of DNA sequences and its applications to phylogenetic analysis.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Next Generation Sequencing & Applications

Author(s): Yang Y, Zhang Y, Jia M, Li C, Meng L

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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.
This article was published in Comb Chem High Throughput Screen and referenced in Journal of Next Generation Sequencing & Applications

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