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的化学差异之间的有趣关系。除了需要进一步研究的少数例外情况外，人们可以得出结论，两个密码子之间的高突变概率与相当相关的氨基酸一起发生，因此损害较小。在编码区内，除了已知的密码子到氨基酸的映射外，我们没有发现任何错误纠正程序。突变概率还导致通信通道描述，并且将容量与20个氨基酸给出的最小所需信息含量进行比较。我们根据“嵌入蛋白”的生物学例子修改了所有的Lempel-Ziv源编码算法，即，我们利用数据中的对称性将它们修改为双向的。利用下一代测序技术，我们发现i)编码单元的空间组织是基因表达一致性的决定因素；ii)距离较近的不同编码单元在DNA超螺旋度的生理水平上表现出最佳活性；iii)我们提出了DNA作为双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（DNA熔化能量和超卷曲）和数字信息（基因的不同功能类别）模式的数据集，并整合了基因的物理化学性质及其功能内容；v)我们检测到介导3D DNA结构转化为表达模式的瞬态染色体结构域；(6)将DNA模拟信息转化为数字线性编码是协调基因转录的基本装置。使用多维尺度作为工具来研究密码子和氨基酸之间的距离，稀疏子空间聚类将在第二个项目阶段进行研究。然而，对所得结果的解释将是至关重要的。我们将研究启动子区域的编码特性，并将玻尔兹曼熵和香农熵进行比较，以期获得更多的见解。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。香农熵和玻尔兹曼熵之间的关系被视为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.