Hidden Addressing Encoding for DNA Storage

Abstract

DNA is a natural storage medium with the advantages of high storage density and long service life compared with traditional media. DNA storage can meet the current storage requirements for massive data. Owing to the limitations of the DNA storage technology, the data need to be converted into short DNA sequences for storage. However, in the process, a large amount of physical redundancy will be generated to index short DNA sequences. To reduce redundancy, this study proposes a DNA storage encoding scheme with hidden addressing. Using the improved fountain encoding scheme, the index replaces part of the data to realize hidden addresses, and then, a 10.1 MB file is encoded with the hidden addressing. First, the Dottup dot plot generator and the Jaccard similarity coefficient analyze the overall self-similarity of the encoding sequence index, and then the sequence fragments of GC content are used to verify the performance of this scheme. The final results show that the encoding scheme indexes with overall lower self-similarity, and the local thermodynamic properties of the sequence are better. The hidden addressing encoding scheme proposed can not only improve the utilization of bases but also ensure the correct rate of DNA storage during the sequencing and decoding processes.

Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads

“…To reduce writing and reading costs, recent works adopted the encoding schemes of DNA Fountain ( Erlich and Zielinski 2017 ), which employed Reed–Solomon (RS) codes and fountain codes [especially Luby transform (LT) codes] ( Anavy et al 2019 , Koch et al 2020 , Jeong et al 2021 , Cao et al 2022 , Song et al 2022 , Wang et al 2022 ). This coding scheme is an effective method to correct errors and recover lost strands (i.e.…”

Storing Images in DNA via base128 Encoding

“…During the reading of data stored in DNA, the base composition of the DNA sequence had an important impact on the results of DNA sequencing . Compared with the deviated GC content sequence, the balanced GC content encoding sequence had higher coverage and less of a secondary structure, which is promising to achieve higher-quality reads under the same sequencing coverage. ,, Moreover, DNA sequences locally satisfying the GC content balance can further improve the accuracy of data reading . To validate whether the sequences adhere to the local GC content balance requirement, we randomly selected equidistant base sequences from the Lena image data.…”

“…Through an exclusion or operation, the encoding sequence between seeds met the GC content and homopolymer constraints, and the NID was 1.57 bits/nt. To reduce data redundancy, Wang et al further improved the fountain code by replacing the index with partial data to improve the accuracy of sequencing and decoding. Furthermore, Cao et al designed encodings using graph convolutional networks and self-attention, achieving high storage density and read-write efficiency.…”

Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits

“…1,2 Based on the principle of complementary base pairing, DNA molecules are being used in frontier areas such as neural networks, 3,4 information encryption 5,6 disease detection 7,8 and DNA storage. [9][10][11] With great potential for information transfer and processing, DNA molecules enable molecular logic circuits, [12][13][14] tiles, [15][16][17] walker machines, [18][19][20] and protein interaction. 21 Molecular logic circuits are circuits that perform basic logic operations, and they are often used to implement functions such as parity checking, 22,23 logic computations, 24,25 drug delivery 26,27 and biosensing.…”