基于3-ary Huffman编码的蛋白质序列比较方法

IF 2.9 2区化学 Q2 CHEMISTRY, MULTIDISCIPLINARY

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-04-01 DOI:10.46793/match.90-2.357q

Zhaohui Qi, Yingqiang Ning, Yinmei Huang

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引用次数: 0

摘要

基于三进位霍夫曼编码算法，提出了一种蛋白质序列的数字映射方法。首先，根据给定蛋白质序列中20个氨基酸的频率特征，定义3-ary Huffman树;由3-ary Huffman树构建的20个氨基酸的0-2编码可以将长蛋白质序列转换成一对一的0-2数字序列。根据0-2数字序列中20个氨基酸的0-2编码的频率特征和分布信息，设计了40维载体来表征蛋白质序列。接下来，利用所提出的数字作图方法对9个ND6蛋白的相似性比较、2009年甲型H1N1流感大流行病毒2020年1月至2022年6月的进化趋势分析和95个冠状病毒基因的进化分析进行了3个单独的应用。结果表明了该方法的有效性。

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Protein Sequence Comparison Method Based on 3-ary Huffman Coding

Based on 3-ary Huffman coding algorithm, we propose a digital mapping method of protein sequence. Firstly, a 3-ary Huffman tree is defined by the frequency characteristic of 20 amino acids in given protein sequences. The 0-2 codes of 20 amino acids constructed by the 3-ary Huffman tree can convert long protein sequences into one-to-one 0-2 digital sequences. According to the frequency characteristic and the distribution information of 0-2 codes of 20 amino acids in the 0-2 digital sequences, we design the 40-dimensional vectors to characterize the protein sequences. Next, the proposed digital mapping method is used to perform three separate applications, similarity comparison of nine ND6 proteins, evolutionary trend analysis of the 2009 pandemic Human influenza A (H1N1) viruses from January 2020 to June 2022, and the evolution analysis of 95 coronavirus genes. The results illustrate the utility of the proposed method.

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来源期刊

Match-Communications in Mathematical and in Computer Chemistry 化学-化学综合

CiteScore

4.40

自引率

26.90%

发文量

审稿时长

2 months

期刊介绍： MATCH Communications in Mathematical and in Computer Chemistry publishes papers of original research as well as reviews on chemically important mathematical results and non-routine applications of mathematical techniques to chemical problems. A paper acceptable for publication must contain non-trivial mathematics or communicate non-routine computer-based procedures AND have a clear connection to chemistry. Papers are published without any processing or publication charge.