The DNA from a Coding Perspektive

到目前为止，我们已经发现了密码子突变概率与相应氨基酸化学差异之间的有趣关系。除了少数需要进一步研究的例外，我们可以得出结论，两个密码子之间的高突变概率与相当相关的氨基酸一起，因此损伤较小。在编码区域内，除了已知的密码子到氨基酸的映射之外，我们没有发现任何纠错程序。突变概率还导致通信信道描述，并且将容量与由20个氨基酸给出的最小所需信息内容进行比较。我们修改了所有Lempel-Ziv源编码算法，遵循“嵌入蛋白质”的生物学示例，即，我们利用数据中的对称性将它们修改为双向的。使用下一代测序，我们发现i）编码单元的空间组织是连贯基因表达的决定因素; ii）紧密接近的发散编码单元在DNA超螺旋性的生理水平上显示出最佳活性; iii）我们开发了DNA作为双重模拟和数字信息载体的新概念; iv）我们生成了对应于模拟信息模式的数据集（DNA熔解能和超螺旋）和数字信息（不同功能类别的基因）并将基因的理化性质与其功能内容整合; v）我们检测了介导3D DNA结构转化为表达模式的瞬时染色体结构域; vi）我们证明了DNA模拟信息到数字线性代码的转换是协调基因转录的基本装置。使用多维标度作为研究密码子和氨基酸之间距离的工具，稀疏子空间聚类将在项目第二阶段进行研究。然而，对所得结果的解释将是至关重要的。启动子区域的编码特性将被研究，玻尔兹曼熵和香农熵之间的比较有望提供更多的见解。我们渴望知道DNA的物理化学参数（DNA语法）是如何转化为遗传功能（DNA语义）的。Shannon熵和玻尔兹曼熵之间的关系被认为是深入了解保护机制和基因表达的关键。

So far, we have found interesting relationships between mutation probabilities of codons and chemical differences in corresponding amino acids. Up to a few exceptions that need to be studied further, one can conclude that high mutational probabilities between two codons go together with rather relatedamino-acids, hence less damage. Within the coding regions, we did not find any error-correction procedure apart from the known mapping of codons to amino acids. Mutation probabilities also lead to a communication channel description and the capacity is compared to the minimum required information content given by the 20 amino acids.We modified all Lempel-Ziv source coding algorithms following the biological example of "embedded proteins", i.e., we modified them to be bi-directional making use of symmetries in the data.Using Next Generation Sequencing we found that i) the spatial organization of coding units is a determinant of coherent gene expression; ii) the divergent coding units in close proximity show optimal activity at physiological levels of DNA superhelicity; iii) we developed a novel concept of the DNA as a carrier of dual - analog and digital - information; iv) we generated datasets corresponding to patterns of analog information (DNA melting energy and supercoiling) and digital information (distinct functionalclasses of genes) and integrated the physicochemical properties of the genes with their functional content; v) we detected transient chromosomal domains mediating the conversion of the 3D DNA structures into expression patterns; vi) we showed that conversion of the DNA analog information into the digital linear code is a basic device coordinating the gene transcription.Having used multidimensional scaling as a tool to investigate distances between codons and amino-acids, sparse subspace clustering will be studied in the second project phase. However, the interpretation of the obtained results will be essential. Coding properties of promoter regions will be looked into and the comparison between Boltzmann and Shannon entropy is expected to give some more insights. We are keen to know how the physicochemical parameters of the DNA (DNA syntax) are converted into genetic function (DNA semantics). The relationship between Shannon and Boltzmann entropy is seen as the key to obtain insights into protection mechanisms and gene expression.