College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.
Evol Bioinform Online. 2014 Jun 12;10:87-96. doi: 10.4137/EBO.S14713. eCollection 2014.
Sequence comparison is one of the foundations in bioinformatics, which can be used to study evolutionary relations among the sequences. In this study, a 2D spectrum-like graphical representation of protein sequences is presented based on the hydrophobicity scale of amino acids. The frequencies of amplitudes of 4-subsequences are adopted to characterize a spectrum-like graph, and a 17D vector is used as the descriptor of protein sequence. The χ(2) value of compatibility test is performed. New similarity analysis approach is illustrated on the all protein sequences, which are encoded by the mitochondrion genome of 20 different species. Finally, comparison with the ClustalW method shows the utility of our method.
序列比对是生物信息学的基础之一，可用于研究序列之间的进化关系。本研究基于氨基酸的疏水性尺度，提出了一种蛋白质序列的二维类光谱图形表示方法。采用 4 元子序列的振幅频率来描述类光谱图，并将 17 维向量作为蛋白质序列的描述符。进行了 χ(2) 值兼容性检验。新的相似性分析方法应用于 20 个不同物种线粒体基因组编码的所有蛋白质序列。最后，与 ClustalW 方法的比较表明了我们方法的实用性。
