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The DNA from a Coding Perspective

从编码角度看 DNA

基本信息

批准号：
328529227
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：
Research Grants
财政年份：
2017
资助国家：
德国
起止时间：
2016-12-31 至 2022-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/328529227?language=en
关键词：
DNA Coding Perspective

项目摘要

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.

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转变为一个具有模拟特征的数字实体。这些类似物的特征源于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。这些物理或信息论性质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，蛋白质和DNA结构的这种双重编码在很大程度上是独立的。在之前的项目中，我们能够证明基因在细菌染色体上的战略定位，以利用不同染色体区域的DNA特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，因为这无论如何对于所考虑的编码是必不可少的，但从密码子和氨基酸之间的映射开始，通过存储器沿着由马尔可夫模型或上下文树建模的DNA链，直到被解释为代码图的调节网络。为此，我们可以从我们在UEP编码方面的经验以及我们对DNA的模拟和数字特性的理解中获益。

项目成果

期刊论文数量（7）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Multilevel capacities for the codon mutation channel

密码子突变通道的多级能力

DOI：
10.1109/istc.2018.8625354
发表时间：
2018
期刊：
2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing (ISTC)
影响因子：
0
作者：
Dawit Nigatu;Werner Henkel
通讯作者：
Werner Henkel

Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers