The DNA from a Coding Perspektive

从编码角度看DNA

• 批准号: 214186146
• 负责人: Professor Dr.-Ing. Werner Henkel
• 金额: --
• 依托单位: Department of Computer Science and Electrical Engineering
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2012
• 资助国家: 德国
• 起止时间: 2011-12-31 至 2014-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/214186146?language=en
• 关键词: DNA; Coding; Perspektive

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.

到目前为止，我们发现密码子的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，一个人可以得出结论，两个密码子之间的高突变概率与相当相关的氨基酸一起进行，因此损坏更少。在编码区域内，除了将密码子与氨基酸的已知映射绘制外，我们没有发现任何错误校正程序。突变概率也会导致通信渠道的描述，并将能力与20个氨基酸给出的最低要求的信息内容进行比较。我们修改了所有LEMPEL-ZIV源编码算法，按照“嵌入蛋白质嵌入蛋白”的生物学示例，即将其修改为对Spemmetries进行双向编码。相干基因表达的决定因素； ii）在DNA超固醇的生理水平上，近距离的发散编码单元显示出最佳的活性； iii）我们开发了一个新颖的DNA概念，作为双 - 模拟和数字信息的载体； iv）我们生成了对应于模拟信息模式（DNA熔化能量和超串联）和数字信息（基因的不同功能频道）的数据集，并将基因的理化特性与其功能含量相结合； v）我们检测到介导3D DNA结构转化为表达模式的瞬时染色体结构域。 vi）我们表明，将DNA模拟信息转换为数字线性代码是一种基本的设备，可以协调基因转录。使用多维缩放作为研究密码子与氨基酸之间的距离，将在第二个项目阶段研究稀疏的子空间聚类。但是，对获得的结果的解释至关重要。将研究启动子区域的编码属性，并有望提供更多的见解。我们渴望知道如何将DNA（DNA语法）的物理化学参数转换为遗传功能（DNA语义）。香农和鲍尔茨曼熵之间的关系被视为获得对保护机制和基因表达的洞察力的关键。