"Galaxy" encoding: toward high storage density and low cost.

IF 3.7 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS IEEE Transactions on NanoBioscience Pub Date : 2024-10-28 DOI:10.1109/TNB.2024.3481504
Xuncai Zhang, Yunfei Lu
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Abstract

DNA is considered one of the most attractive storage media because of its excellent reliability and durability. Early encoding schemes lacked flexibility and scalability. To address these limitations, we propose a combination of static mapping and dynamic encoding, named "Galaxy" encoding. This scheme uses both the "dual-rule interleaving" algorithm and the "twelve-element Huffman rotational encoding" algorithm. We tested it with "Shakespeare Sonnets" and other files, achieving an encoding information density of approximately 2.563 bits/nt. Additionally, the inclusion of Reed-Solomon error-correcting codes can correct nearly 5% of the errors. Our simulations show that it supports various file types (.gz, .tar, .exe, etc.). We also analyzed the cost and fault tolerance of "Galaxy" encoding, demonstrating its high coding efficiency and ability to fully recover original information while effectively reducing the costs of DNA synthesis and sequencing.

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"银河 "编码:实现高存储密度和低成本。
DNA 因其出色的可靠性和耐用性而被认为是最具吸引力的存储介质之一。早期的编码方案缺乏灵活性和可扩展性。为了解决这些局限性,我们提出了一种静态映射和动态编码相结合的方案,命名为 "银河 "编码。该方案同时使用了 "双规则交错 "算法和 "十二元素哈夫曼旋转编码 "算法。我们用 "莎士比亚十四行诗 "和其他文件对其进行了测试,编码信息密度约为 2.563 bits/nt。此外,加入里德-所罗门纠错码可纠正近 5%的错误。我们的模拟显示,它支持各种文件类型(.gz、.tar、.exe 等)。我们还分析了 "银河 "编码的成本和容错性,证明其编码效率高,能够完全恢复原始信息,同时有效降低 DNA 合成和测序的成本。
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来源期刊
IEEE Transactions on NanoBioscience
IEEE Transactions on NanoBioscience 工程技术-纳米科技
CiteScore
7.00
自引率
5.10%
发文量
197
审稿时长
>12 weeks
期刊介绍: The IEEE Transactions on NanoBioscience reports on original, innovative and interdisciplinary work on all aspects of molecular systems, cellular systems, and tissues (including molecular electronics). Topics covered in the journal focus on a broad spectrum of aspects, both on foundations and on applications. Specifically, methods and techniques, experimental aspects, design and implementation, instrumentation and laboratory equipment, clinical aspects, hardware and software data acquisition and analysis and computer based modelling are covered (based on traditional or high performance computing - parallel computers or computer networks).
期刊最新文献
Electrospun Stannic Oxide Nanofiber Thin-Film Based Sensing Device for Monitoring Functional Behaviours of Adherent Mammalian Cells. "Galaxy" encoding: toward high storage density and low cost. 2024 Index IEEE Transactions on NanoBioscience Vol. 23 Table of Contents Front Cover
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