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DNA sequence similarity analysis using image texture analysis based on first-order statistics.
Journal of Molecular Graphics and Modelling ( IF 2.7 ) Pub Date : 2020-05-03 , DOI: 10.1016/j.jmgm.2020.107603
Emre Delibaş 1 , Ahmet Arslan 2
Affiliation  

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.



中文翻译:

使用基于一阶统计的图像纹理分析进行DNA序列相似性分析。

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,都需要进行相似度计算。无序列比对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的相似度计算进行DNA序列相似度分析研究的新方法。假设这些计算可适用于无比对的DNA序列相似性分析方法,此处使用纹理分析方法(是数字图像处理方法的子集)。通过分配给DNA序列中核苷酸的值来创建灰度纹理。使用基于直方图的基于直方图的纹理分析,在这些纹理之间进行了相似度计算。我们获得了3种不同长度的不同DNA数据集的纹理特征,并计算了相似度矩阵。我们的方法揭示的系统发育关系表明,我们的树木与基于序列比对的MEGA软件的​​结果相似。我们的发现表明,纹理分析指标可用于表征DNA序列。并计算相似度矩阵 我们的方法揭示的系统发育关系表明,我们的树木与基于序列比对的MEGA软件的​​结果相似。我们的发现表明,纹理分析指标可用于表征DNA序列。并计算相似度矩阵 我们的方法揭示的系统发育关系表明,我们的树木与基于序列比对的MEGA软件的​​结果相似。我们的发现表明,纹理分析指标可用于表征DNA序列。

更新日期:2020-05-03
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