Afreixo Vera, Rodrigues João M O S, Bastos Carlos A C
University of Aveiro, 3810-193 Aveiro, Portugal.
J Integr Bioinform. 2014 Oct 23;11(3):250. doi: 10.2390/biecoll-jib-2014-250.
Some previous studies point to the extension of Chargaff’s second rule (the phenomenon of symmetry) to words of large length. However, in random sequences generated by an independent symbol model where the probability of occurrence of complementary nucleotides is the same, we expect that the phenomenon of symmetry holds for all word lengths. In this work, we measure the symmetry above that expected in independence contexts (exceptional symmetry), for several organisms: viruses; archaea; bacteria; eukaryotes. We also create 27 control scenarios with the same length of each genome under study. The results for each organism were compared to those obtained in control scenarios. We created a new organism genomic signature consisting of a vector of the measures of exceptional symmetry for words of lengths 1 through 12. We show that the proposed signature is able to capture essential relationships between organisms.
一些先前的研究指出了查加夫第二规则（对称性现象）在长单词中的延伸。然而，在由独立符号模型生成的随机序列中，互补核苷酸出现的概率相同，我们预期对称性现象适用于所有单词长度。在这项工作中，我们测量了几种生物体（病毒、古细菌、细菌、真核生物）相对于独立环境中预期的对称性（异常对称性）。我们还创建了27个控制场景，每个研究的基因组长度相同。将每个生物体的结果与在控制场景中获得的结果进行比较。我们创建了一种新的生物体基因组特征，它由长度从1到12的单词的异常对称性度量向量组成。我们表明，所提出的特征能够捕捉生物体之间的基本关系。
