Fimmel Elena, Danielli Alberto, Strüngmann Lutz
Institute of Applied Mathematics, Faculty of Computer Sciences, Mannheim University of Applied Sciences, 68163 Mannheim, Germany.
J Theor Biol. 2013 Nov 7;336:221-30. doi: 10.1016/j.jtbi.2013.07.027. Epub 2013 Aug 26.
Dichotomic classes arising from a recent mathematical model of the genetic code allow to uncover many symmetry properties of the code, and although theoretically derived, they permitted to build statistical classifiers able to retrieve the correct translational frame of coding sequences. Herein we formalize the mathematical properties of these classes, first focusing on all the possible decompositions of the 64 codons of the genetic code into two equally sized dichotomic subsets. Then the global framework of bijective transformations of the nucleotide bases is discussed and we clarify when dichotomic partitions can be generated. In addition, we show that the parity dichotomic classes of the mathematical model and complementarity dichotomic classes obtained in the present article can be formalized in the same algorithmic way the dichotomic Rumer's degeneracy classes. Interestingly, we find that the algorithm underlying dichotomic class definition mirrors biochemical features occurring at discrete base positions in the decoding center of the ribosome.
源自遗传密码最新数学模型的二分法类别有助于揭示该密码的许多对称特性，尽管这些类别是从理论上推导出来的，但它们使得构建能够检索编码序列正确翻译框架的统计分类器成为可能。在此，我们形式化了这些类别的数学性质，首先关注遗传密码64个密码子分解为两个大小相等的二分法子集的所有可能情况。然后讨论了核苷酸碱基双射变换的全局框架，并阐明了何时可以生成二分法划分。此外，我们表明本文中得到的数学模型的奇偶二分法类别和互补二分法类别可以用与二分法鲁默简并类别相同的算法方式进行形式化。有趣的是，我们发现二分法类别定义所依据的算法反映了核糖体解码中心离散碱基位置上出现的生化特征。
