{"title":"\"Galaxy\" encoding: toward high storage density and low cost.","authors":"Xuncai Zhang, Yunfei Lu","doi":"10.1109/TNB.2024.3481504","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"IEEE Transactions on NanoBioscience","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1109/TNB.2024.3481504","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
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.
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).