Bielińska-Wąż Dorota, Wąż Piotr, Lass Anna, Karamon Jacek
Department of Radiological Informatics and Statistics, Medical University of Gdańsk, 80-210 Gdańsk, Poland.
Department of Nuclear Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland.
Life (Basel). 2022 Jun 10;12(6):877. doi: 10.3390/life12060877.
The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (), cytochrome b (), and cytochrome c oxidase subunit 1 (), are analyzed. The sequences are represented by sets of material points in a 4D space, i.e., 4D-dynamic graphs. As a visualization of the sequences, projections of the graphs into 3D space are shown. The differences between 3D graphs corresponding to European, Asian, and American haplotypes are small. Numerical characteristics () applied in the studies can recognize the differences. The concept of creating descriptors of 4D-dynamic graphs has been borrowed from classical dynamics; these are coordinates of the centers or mass and moments of inertia of 4D-dynamic graphs. Based on these descriptors, classification maps are constructed. The concentrations of points in the maps indicate one Polish haplotype (EmPL9) of Asian origin.
我们最近开发的一种无比对生物信息学方法——DNA/RNA序列的4D动态表示法，已被用于研究波兰赤狐的遗传多样性。分析了三个线粒体基因的序列，即NADH脱氢酶亚基2（）、细胞色素b（）和细胞色素c氧化酶亚基1（）。这些序列由4D空间中的物质点集表示，即4D动态图。作为序列的可视化，展示了图在3D空间中的投影。对应于欧洲、亚洲和美洲单倍型的3D图之间的差异很小。研究中应用的数值特征（）可以识别这些差异。创建4D动态图描述符的概念借鉴了经典动力学；这些是4D动态图的质心坐标和转动惯量。基于这些描述符构建分类图。图中各点的聚集表明有一种亚洲起源的波兰单倍型（EmPL9）。
