颜林林 (2023-04-30 10:31):
#paper doi:10.1109/TNB.2023.3254514 IEEE transactions on nanobioscience, 2023, RBS: A Rotational Coding Based on Blocking Strategy for DNA Storage. 利用DNA作为介质研发数据存储方案,是近几年的热点之一,许多研究所和公司都竞相开展,但投入和进展却层次不齐。这也是我个人比较感兴趣的方向之一,因此关注到最近刚发表出来的这篇文章,顺便点评一下。虽然这篇文章并不算多出彩,也没有什么重大突破,但它是一篇纯算法的概念验证工作,不涉及到分子实验,倒是比较适合我这种业余感兴趣者效仿。用DNA介质存储数据,面临各种现实问题,比如GC含量需要限制在一定范围,过高或过低的GC含量,都会在合成和测序上导致问题,再比如不能有连续重复片段等。也因此,对数据进行DNA字母的编码,不能简单随便设置某种一一对应规则,而需要同时考虑各类分子特性限制。本文提出了一种数据编解码算法RBS,并使用文本、图片数据测试,评估诸如GC含量、重复片段数量、汉明距离、自由能等,以确认该算法用于DNA存储的可行性和效率。
RBS: A Rotational Coding Based on Blocking Strategy for DNA Storage
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Abstract:
The data volume of global information has grown exponentially in recent years, but the development of silicon-based memory has entered a bottleneck period. Deoxyribonucleic acid (DNA) storage is drawing attention owing to its advantages of high storage density, long storage time, and easy maintenance. However, the base utilization and information density of existing DNA storage methods are insufficient. Therefore, this study proposes a rotational coding based on blocking strategy (RBS) for encoding digital information such as text and images in DNA data storage. This strategy satisfies multiple constraints and produces low error rates in synthesis and sequencing. To illustrate the superiority of the proposed strategy, it was compared and analyzed with existing strategies in terms of entropy value change, free energy size, and Hamming distance. The experimental results show that the proposed strategy has higher information storage density and better coding quality in DNA storage, so it will improve the efficiency, practicality, and stability of DNA storage.
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