Afreixo Vera, Rodrigues João M O S, Bastos Carlos A C, Tavares Ana H M P, Silva Raquel M
iBiMED-Institute of Biomedicine, IEETA-Institute of Electronic Engineering and Informatics of Aveiro, CIDMA- Center for Research and Development in Mathematics and Applications, Department of Mathematics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
Interdiscip Sci. 2017 Mar;9(1):14-23. doi: 10.1007/s12539-016-0200-9. Epub 2016 Nov 19.
Single-strand DNA symmetry is pointed as a universal law observed in the genomes from all living organisms. It is a somewhat broadly defined concept, which has been refined into some more specific measurable effects. Here we discuss the exceptional symmetry effect. Exceptional symmetry is the symmetry effect beyond that expected in independence contexts, and it can be measured for each word, for each equivalent composition group, or globally, combining the effects of all possible words of a given length. Global exceptional symmetry was found in several species, but there are genomic words with no exceptional symmetry effect, whereas others show a very high exceptional symmetry effect. In this work, we discuss a measure to evaluate the exceptional symmetry effect by symmetric word pair, and compare it with others. We present a detailed study of the exceptional symmetry by symmetric pairs and take the CG content into account. We also introduce and discuss the exceptional symmetry profile for the DNA of each organism, and we perform a multiple comparison for 31 genomes: 7 viruses; 5 archaea; 5 bacteria; 14 eukaryotes.
单链DNA对称性被视为在所有生物基因组中观察到的普遍规律。这是一个定义较为宽泛的概念，已细化为一些更具体的可测量效应。在此我们讨论特殊对称性效应。特殊对称性是超出独立情境预期的对称性效应，它可以针对每个单词、每个等效组成组或整体进行测量，将给定长度的所有可能单词的效应结合起来。在几个物种中发现了整体特殊对称性，但存在一些基因组单词没有特殊对称性效应，而其他一些则表现出非常高的特殊对称性效应。在这项工作中，我们讨论一种通过对称单词对来评估特殊对称性效应的方法，并将其与其他方法进行比较。我们通过对称对详细研究特殊对称性，并考虑CG含量。我们还引入并讨论了每个生物体DNA的特殊对称性概况，并对31个基因组进行了多重比较：7种病毒；5种古细菌；5种细菌；14种真核生物。
