2D FFT和DTW在蛋白质序列比较中的应用。

IF 1.9 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Jayanta Pal, Soumen Ghosh, Bansibadan Maji, Dilip Kumar Bhattacharya
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引用次数: 0

摘要

蛋白质序列比较对研究人员来说仍然是一项具有挑战性的工作,因为基因组序列中存在20个氨基酸,而只有4个核苷酸,因此计算复杂。此外,不同物种的蛋白质序列具有不同的长度;它为研究人员开发比较蛋白质序列的方法,特别是无比对方法带来了额外的变化。在这项工作中,通过图形表示开发了一种比较蛋白质序列的有效技术。首先,基于极性类别对基数为4的20个氨基酸进行分类分组,以将代表性范围从20缩小到4。然后,提出了一种基于两象限笛卡尔系统的单位向量技术,以提供蛋白质序列的新的二维图形表示。现在,提出了两种方法来处理来自不同物种的不同长度的蛋白质序列:一种使用动态时间扭曲(DTW),而另一种使用二维快速傅立叶变换(2D FFT)。接下来,使用基于对称距离(SD)和计算速度的两个评估标准定量测量来分析这两种技术的有效性。在两种方法下对9个ND4、9个ND5、9个ND 6、12个杆状病毒和24个TF蛋白的5个数据集进行分析。研究发现,基于FFT的方法产生了与DTW相同的结果,但计算时间更短。研究发现,该方法的结果与已知的生物学参考文献一致。此外,本方法产生了比现有方法更好的聚类。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Use of 2D FFT and DTW in Protein Sequence Comparison

Use of 2D FFT and DTW in Protein Sequence Comparison

Use of 2D FFT and DTW in Protein Sequence Comparison

Protein sequence comparison remains a challenging work for the researchers owing to the computational complexity due to the presence of 20 amino acids compared with only four nucleotides in Genome sequences. Further, protein sequences of different species are of different lengths; it throws additional changes to the researchers to develop methods, specially alignment-free methods, to compare protein sequences. In this work, an efficient technique to compare protein sequences is developed by a graphical representation. First, the classified grouping of 20 amino acids with a cardinality of 4 based on polar class is considered to narrow down the representational range from 20 to 4. Then a unit vector technique based on a two-quadrant Cartesian system is proposed to provide a new two-dimensional graphical representation of the protein sequence. Now, two approaches are proposed to cope with the varying lengths of protein sequences from various species: one uses Dynamic Time Warping (DTW), while the other one uses a two-dimensional Fast Fourier Transform (2D FFT). Next, the effectiveness of these two techniques is analyzed using two evaluation criteria—quantitative measures based on symmetric distance (SD) and computational speed. An analysis is performed on five data sets of 9 ND4, 9 ND5, 9 ND6, 12 Baculovirus, and 24 TF proteins under the two methods. It is found that the FFT-based method produces the same results as DTW but in less computational time. It is found that the result of the proposed method agrees with the known biological reference. Further, the present method produces better clustering than the existing ones.

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来源期刊
The Protein Journal
The Protein Journal 生物-生化与分子生物学
CiteScore
5.20
自引率
0.00%
发文量
57
审稿时长
12 months
期刊介绍: The Protein Journal (formerly the Journal of Protein Chemistry) publishes original research work on all aspects of proteins and peptides. These include studies concerned with covalent or three-dimensional structure determination (X-ray, NMR, cryoEM, EPR/ESR, optical methods, etc.), computational aspects of protein structure and function, protein folding and misfolding, assembly, genetics, evolution, proteomics, molecular biology, protein engineering, protein nanotechnology, protein purification and analysis and peptide synthesis, as well as the elucidation and interpretation of the molecular bases of biological activities of proteins and peptides. We accept original research papers, reviews, mini-reviews, hypotheses, opinion papers, and letters to the editor.
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