New Construction of Balanced Codes Based on Weights of Data for DNA Storage

被引:0
作者
Lu, Xiaozhou [1 ]
Kim, Sunghwan [1 ]
机构
[1] Univ Ulsan, Dept Elect Elect & Comp Engn, Ulsan 44610, South Korea
关键词
Balanced codes; DNA storage; GC-balanced; weight distribution; CONSTRAINED CODES; ERROR-CORRECTION; HIGH-CAPACITY; LENGTH;
D O I
10.1109/TETC.2023.3293477
中图分类号
TP [自动化技术、计算机技术];
学科分类号
0812 ;
摘要
As maintaining a proper balanced GC content is crucial for minimizing errors in DNA storage, constructing GC-balanced DNA codes has become an important research topic. In this article, we propose a novel code construction method based on the weight distribution of the data, which enables us to construct GC-balanced DNA codes. Additionally, we introduce a specific encoding process for both balanced and imbalanced data parts. One of the key differences between the proposed codes and existing codes is that the parity lengths of the proposed codes are variable depending on the data parts, while the parity lengths of existing codes remain fixed. To evaluate the effectiveness of the proposed codes, we compare their average parity lengths to those of existing codes. Our results demonstrate that the proposed codes have significantly shorter average parity lengths for DNA sequences with appropriate GC contents.
引用
收藏
页码:973 / 984
页数:12
相关论文
共 18 条
[1]   Forward Error Correction for DNA Data Storage [J].
Blawat, Meinolf ;
Gaedke, Klaus ;
Huetter, Ingo ;
Chen, Xiao-Ming ;
Turczyk, Brian ;
Inverso, Samuel ;
Pruitt, Benjamin W. ;
Church, George M. .
INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE 2016 (ICCS 2016), 2016, 80 :1011-1022
[2]   DNA storage: research landscape and future prospects [J].
Dong, Yiming ;
Sun, Fajia ;
Ping, Zhi ;
Ouyang, Qi ;
Qian, Long .
NATIONAL SCIENCE REVIEW, 2020, 7 (06) :1092-1107
[3]   DNA Fountain enables a robust and efficient storage architecture [J].
Erlich, Yaniv ;
Zielinski, Dina .
SCIENCE, 2017, 355 (6328) :950-953
[4]   Towards practical, high-capacity, low-maintenance information storage in synthesized DNA [J].
Goldman, Nick ;
Bertone, Paul ;
Chen, Siyuan ;
Dessimoz, Christophe ;
LeProust, Emily M. ;
Sipos, Botond ;
Birney, Ewan .
NATURE, 2013, 494 (7435) :77-80
[5]   A Characterization of the DNA Data Storage Channel [J].
Heckel, Reinhard ;
Mikutis, Gediminas ;
Grass, Robert N. .
SCIENTIFIC REPORTS, 2019, 9 (1)
[6]   DNA-Based Storage: Trends and Methods [J].
Yazdi, S. M. Hossein Tabatabaei ;
Kiah, Han Mao ;
Garcia-Ruiz, Eva ;
Ma, Jian ;
Zhao, Huimin ;
Milenkovic, Olgica .
IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, 2015, 1 (03) :230-248
[7]   Properties and Constructions of Constrained Codes for DNA-Based Data Storage [J].
Immink, Kees A. Schouhamer ;
Cai, Kui .
IEEE ACCESS, 2020, 8 :49523-49531
[8]   EFFICIENT BALANCED CODES. [J].
Knuth, Donald E. .
IEEE Transactions on Information Theory, 1986, IT-32 (01) :51-53
[9]   DNA assembly for nanopore data storage readout [J].
Lopez, Randolph ;
Chen, Yuan-Jyue ;
Dumas, Siena ;
Yekhanin, Ang Sergey ;
Makarychev, Konstantin ;
Racz, Miklos Z. ;
Seelig, Georg ;
Strauss, Karin ;
Ceze, Luis .
NATURE COMMUNICATIONS, 2019, 10 (1)
[10]   A CLASS OF MULTIPLE-ERROR-CORRECTING CODES AND THE DECODING SCHEME [J].
REED, IS .
IRE TRANSACTIONS ON INFORMATION THEORY, 1954, (04) :38-49