Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition

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• 作者：Yujuan Huang ; Lianping Yang ; Tianming Wang
• 关键词：DNA ; Dinucleotide ; LZ complexity ; Phylogenetic tree
• 刊名：Journal of Theoretical Biology
• 出版年：2011
• 出版时间：21 January 2011
• 年：2011
• 卷：269
• 期：1
• 页码：217-223
• 全文大小：258 K

文摘

The main work of this paper is to propose a new theory and method, which is based on the idea of the pseudo-amino acid composition, for phylogenetic analysis of DNA primary sequences. In our method, we revise the part of the occurrence frequency of 20 amino acids in the method of the pseudo-amino acid composition by replacing the frequency of 16 dinucleotides. And we select eight LZ complexity factors of eight (0,1) sequences of a DNA primary sequence as PseAA components. Finally, we characterize a DNA sequence with a 24-dimensional vector. We reconstruct the phylogenetic trees of two datasets. The results show that our method is efficient and significant.