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基于一阶统计量的图像纹理分析用于DNA序列相似性分析。

DNA sequence similarity analysis using image texture analysis based on first-order statistics.

作者信息

Delibaş Emre, Arslan Ahmet

机构信息

Department of Computer Engineering, Faculty of Engineering, Cumhuriyet University, 58140, Sivas, Turkey.

Department of Computer Engineering, Faculty of Engineering, Selçuk University, 42250, Konya, Turkey.

出版信息

J Mol Graph Model. 2020 Sep;99:107603. doi: 10.1016/j.jmgm.2020.107603. Epub 2020 May 3.


DOI:10.1016/j.jmgm.2020.107603
PMID:32442904
Abstract

Similarity is one of the key processes of DNA sequence analysis in computational biology and bioinformatics. In nearly all research that explores evolutionary relationships, gene function analysis, protein structure prediction and sequence retrieving, it is necessary to perform similarity calculations. One major task in alignment-free DNA sequence similarity calculations is to develop novel mathematical descriptors for DNA sequences. In this paper, we present a novel approach to DNA sequence similarity analysis studies using similarity calculations of texture images. Texture analysis methods, which are a subset of digital image processing methods, are used here with the assumption that these calculations can be adapted to alignment-free DNA sequence similarity analysis methods. Gray-level textures were created by the values assigned to the nucleotides in the DNA sequences. Similarity calculations were made between these textures using histogram-based texture analyses based on first-order statistics. We obtained texture features for 3 different DNA data sets of different lengths, and calculated the similarity matrices. The phylogenetic relationships revealed by our method shows our trees to be similar to the results of the MEGA software, which is based on sequence alignment. Our findings show that texture analysis metrics can be used to characterize DNA sequences.

摘要

相似性是计算生物学和生物信息学中DNA序列分析的关键过程之一。在几乎所有探索进化关系、基因功能分析、蛋白质结构预测和序列检索的研究中,都需要进行相似性计算。无比对DNA序列相似性计算中的一项主要任务是为DNA序列开发新颖的数学描述符。在本文中,我们提出了一种使用纹理图像相似性计算进行DNA序列相似性分析研究的新方法。纹理分析方法是数字图像处理方法的一个子集,在此使用时假设这些计算可以适用于无比对DNA序列相似性分析方法。灰度纹理由分配给DNA序列中核苷酸的值创建。使用基于一阶统计的基于直方图的纹理分析在这些纹理之间进行相似性计算。我们为3个不同长度的不同DNA数据集获得了纹理特征,并计算了相似性矩阵。我们的方法揭示的系统发育关系表明我们构建的树与基于序列比对的MEGA软件的结果相似。我们的研究结果表明,纹理分析指标可用于表征DNA序列。

相似文献

[1]
DNA sequence similarity analysis using image texture analysis based on first-order statistics.

J Mol Graph Model. 2020-9

[2]
A novel alignment-free DNA sequence similarity analysis approach based on top-k n-gram match-up.

J Mol Graph Model. 2020-11

[3]
Use of image texture analysis to find DNA sequence similarities.

J Theor Biol. 2018-7-4

[4]
Definition and Usage of Texture Feature for Biological Sequence.

IEEE/ACM Trans Comput Biol Bioinform. 2021

[5]
Alignment-free sequence comparison using N-dimensional similarity space.

Curr Comput Aided Drug Des. 2010-12

[6]
An improved model for whole genome phylogenetic analysis by Fourier transform.

J Theor Biol. 2015-10-7

[7]
A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering.

J Theor Biol. 2014-10-21

[8]
Bayesian coestimation of phylogeny and sequence alignment.

BMC Bioinformatics. 2005-4-1

[9]
K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

Bioinformatics. 2018-5-15

[10]
Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images.

Genomics Proteomics Bioinformatics. 2016-4

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[2]
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J Radiol Prot. 2022-1-12

[3]
Review on the Application of Machine Learning Algorithms in the Sequence Data Mining of DNA.

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