The DNA from a Coding Perspective

在过去的十年里，DNA的前景已经从一个单独的数字编码序列变成了一个具有模拟特征的数字实体。这些模拟特性源于DNA聚合物的物理性质。这四种不同的碱基不仅编码蛋白质的特定组合，同时还赋予聚合物物理和信息理论性质，如熵、热力学稳定性或特定的3D构象。这些物理或信息论特性是基因表达调控的基础。由于蛋白质编码和结构编码的冗余性，这种蛋白质和DNA结构的双重编码在很大程度上是独立的。在前一个项目中，我们能够证明基因被战略性地定位在细菌染色体上，以利用不同染色体区域的DNA属性来区分时间基因表达模式。此外，我们意识到一些方面允许一些不平等的错误保护，我们现在将成为调查的中心，当然，仍然调查模拟和数字信息之间的联系，因为这对于所考虑的编码无论如何都是必不可少的，但否则将研究不同级别的不等错误保护，从密码子和氨基酸之间的映射开始，通过记忆沿着由马尔可夫模型或上下文树建模的DNA链，直到解释为代码图的监管网络。为此，我们可以借鉴我们在UEP编码方面的经验，以及我们对DNA模拟和数字属性的理解基础。

The prospect of DNA has changed over the last decade from a solely digitally coded sequence to a digital entity with analog characteristics. These analog characteristics stem from the physical properties of the DNA polymer. The four different bases not only codein certain combination for proteins but at the same time also assign physical and information theoretic properties like entropy, thermodynamic stability, or specific 3D conformations to the polymer. These physical or information theoretic properties are fundamental for the regulation of gene expression. This dual coding of proteins and DNA structure is largely independent due to the redundancy of the protein coding and structural coding. In the previous project we were able to show that genes are strategically positioned on the bacterial chromosome to utilize DNA properties of distinct chromosomal regions to differentiate temporal gene expression patterns. Furthermore, we realized some aspects that allows for some unequal error protection that we would now make the center of investigations, of course, still investigating the links between analog and digital information, since this is essential for the considered coding anyhow, but otherwise looking into the different levels of unequal error protection, starting from the mapping between codons and amino acids, over memory along the DNA strands modeled by Markov models or context trees, up to the regulatory Networks interpreted as a code graph. To this end, we can profit from our experiences in UEP coding and our basis in the understanding of the analog and digital properties of the DNA.