Application of 2D graphic representation of protein sequence based on Huffman tree method

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• 作者：Zhao-Hui Qi^a ; ^{zhqi_yh2004@yahoo.com.cn}  ; [Author Vitae] ; Jun Feng^a  ; [Author Vitae] ; Xiao-Qin Qi^a  ; [Author Vitae] ; Ling Li^b  ; [Author Vitae]
• 关键词：Protein sequence ; Graphic representation ; Sequence analysis ; Escherichia coli ; Huffman tree
• 刊名：Computers in Biology and Medicine
• 出版年：2012
• 期刊代码：70_00104825
• 类别：med
• 出版时间：May, 2012
• 卷：42
• 期：5
• 页码：556-563
• 文件大小：533 K

摘要

Based on Huffman tree method, we propose a new 2D graphic representation of protein sequence. This representation can completely avoid loss of information in the transfer of data from a protein sequence to its graphic representation. The method consists of two parts. One is about the 0-1 codes of 20 amino acids by Huffman tree with amino acid frequency. The amino acid frequency is defined as the statistical number of an amino acid in the analyzed protein sequences. The other is about the 2D graphic representation of protein sequence based on the 0-1 codes. Then the applications of the method on ten ND5 genes and seven Escherichia coli strains are presented in detail. The results show that the proposed model may provide us with some new sights to understand the evolution patterns determined from protein sequences and complete genomes.