DNA存储文件系统研究进展

昝乡镇; 姚翔宇; 许鹏; 鲍振申; 李先彬; 李晓焱; 刘文斌

doi:10.11999/JEIT220561

DNA存储文件系统研究进展

doi: 10.11999/JEIT220561

1.
广州大学计算科技研究院广州 510006
2.
榆林学院数学与统计学院榆林 719000

基金项目: 国家自然科学基金(62072128, 62002079, 62102104)，榆林市科技局项目(CXY-2020-007)

详细信息

作者简介:
昝乡镇：男，博士生，研究方向为DNA存储、生物信息学

姚翔宇：男，硕士生，研究方向为DNA存储、生物信息学

许鹏：男，副教授，研究方向为DNA存储、生物信息学

鲍振申：男，博士，研究方向为DNA存储、生物信息学

李先彬：男，博士，研究方向为DNA存储、生物信息学

李晓焱：女，副教授，研究方向为DNA存储、几何函数论

刘文斌：男，教授，研究方向为DNA存储、生物信息学

通讯作者:
刘文斌　wbliu6910@gzhu.edu.cn

中图分类号: TN911
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- 被引次数: 0
出版历程
- 收稿日期: 2022-05-07
- 修回日期: 2022-08-23
- 录用日期: 2022-08-25
- 网络出版日期: 2022-08-29
- 刊出日期: 2023-06-10

A Survey on File Architecture in DNA Storage

1.
Institution of Computational Science and Technology, Guangzhou University, Guangzhou 510006, China
2.
School of Mathematics and Statistics, Yulin University , Yulin 719000, China

Funds: The National Natural Science Foundation of China (62072128, 62002079, 62102104), Yulin Science and Technology Bureau Project (CXY-2020-007)

摘要

摘要: DNA存储因具有密度大、保存时间长及维护成本低等优点，为解决海量数据的存储和应用难题提供了“破局”可能。面对大规模数据应用场景，DNA存储必须要解决如何组织、访问和操作数据文件等问题—即文件系统设计问题。该文首先结合计算机文件系统模型，给出了未来DNA存储文件系统模型及具备的特点；然后，系统性综述了DNA存储文件系统研究进展；最后，对未来DNA存储文件系统研究进行了展望。
- DNA存储 /
- 文件系统 /
- 随机访问 /
- 纠错
Abstract: DNA storage technology provides a new way to tackle the problems of massive data storage and application, due to its high density, long durability, and low maintenance cost. To face massive data storage demand, DNA storage has to overcome the problem on how to organize, access and manipulate data files, that is, the design of file system. In this paper, future DNA storage file system model and its characteristics are studied according to computer file system model. Then, the research progress of file system of DNA storage is systematically reviewed. Finally, the perspectives on research direction of future DNA storage file system are discussed.
- DNA Storage /
- File system /
- Random access /
- Error corrections

HTML全文

图 1 DNA存储政府战略规划与重要研究进展

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图 2 计算机文件系统与DNA存储文件系统模型

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图 3 引物数量与文件数量的关系

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图 4 脱水DNA斑点共享地址系统

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图 5 用于DNA存储的主流DNA编辑技术

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表 1 5种特异性PCR扩增引物设计方法性能比较

引物设计方法	方法记号	文件数量(m个引物)	扩增技术	目标文件检索率(%)
1正向，1反向^{[7, 11-13]}	M1	$m/2$	传统PCR	99
1正向，1通用^[14]	M2	$m - 1$	传统PCR	99
1正向，1反向(组合)^[11]	M3	${(m/2)^2}$	传统PCR	99
2正向，1通用^[10]	M4-1	${m^2} - 3m + 2$	巢氏PCR	81
3正向，1通用^[10]	M4-2	${m^3} - 6{m^2} + 11m - 6$	巢氏PCR，磁珠分离，生物素	97
2正向，2反向^[9]	M5	${(m/{\text{4}})^{\text{4}}}$	巢氏PCR	N/A

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表 2 物理排列DNA分子存储方法比较

参考文献	技术特点	存储容量	目标文件检索率(%)
Newman等人^[15]	脱水斑点+数字微流控	1 TB/斑点	66
Antkowiak等人^[16]	二氧化硅包裹脱水斑点+数字微流控	23.5 TB/斑点	99
陈为刚等人^[14]	基于数据块的多个合成池存储	3 MB	99
Banal等人^[17]	单链DNA条形码标记的硅胶胶囊	0.1 kB/胶囊	60～95

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表 3 分子特异性杂交方法性能比较

参考文献	技术特点	目标文件检索率(%)
Lin等人^[19]	T7启动子和单链悬垂构成的DNA分子	99
Banal等人^[17]	单链DNA条形码标记的硅胶胶囊	60～95
Bee等人^[20]	基于图片特征向量的分子杂交搜索	96

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表 4 代表性数据纠错方法性能比较

参考文献	纠错方法	总体逻辑密度 (包含引物或载体骨架)(bit/nt)	最大容忍错误率(%)	测序深度
Bornholt 等人^[39]	连续两序列异或生成冗余序列	0.57	<0.1	40×
Erlich 等人^[27]	DNA喷泉码	1.18	0.15	10.5×
Grass 等人^[42]	RS码	0.83	2	372×
Antkowiak 等人^[44]	多序列比对+RS码	0.8	15	120×
Lenz 等人^[53]	级联码+LDPC码	0.5	18	20×
Press 等人^[51]	哈希+RS码	0.5	3	3×
Song 等人^[52]	图路径搜索	1.5	10	100×
Zan 等人^[56]	调制序列相似性纠错	1.0	40	100×

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表 5 DNA存储数据加密方法性能比较

参考文献	技术特点	生物困难	鲁棒性	加密数据规模	密钥空间
Yang 等人^[57]	一次一密+DNA链置换异或操纵	DNA链置换异或操纵	无	小	$C_{{{\text{4}}^{{\text{25}}}} \times {\text{1000}}}^{{\text{2000}}}$
Zakeri等人^[58]	一代测序、色谱分析、数据隐藏	DNA分子数据隐藏	无	小	9.1×10⁶¹
Zhang 等人^[8]	DNA折纸	DNA分子自组装	无	小	2⁷⁰²
Grass 等人^[60]	AES加密+STR密钥编码	个体识别STR密钥	是	中	2¹³²
Peng 等人^[59]	混沌序列+DNA动态编码+DNA分子接头设计	DNA分子接头设计	无	中	3³×5⁶⁴×2²⁴⁷

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