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Deoxyribonucleic Acid (DNA), with its ultra-high storage density and long durability, is a promising long-term archival storage medium and is attracting much attention today. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. Many encoding schemes have been proposed to enlarge DNA storage capacity by increasing DNA encoding density. However, only increasing encoding density is insufficient because enhancing DNA storage capacity is a multifaceted problem. This paper assumes that random accesses are necessary for practical DNA archival storage. We identify all factors affecting DNA storage capacity under current technologies and systematically investigate the practical DNA storage capacity with several popular encoding schemes. The investigation result shows the collision between primers and DNA payload sequences is a major factor limiting DNA storage capacity. Based on this discovery, we designed a new encoding scheme called Collision Aware Code (CAC) to trade some encoding density for the reduction of primer-payload collisions. Compared with the best result among the five existing encoding schemes, CAC can extricate 120% more primers from collisions and increase the DNA tube capacity from 211.96 GB to 295.11 GB. Besides, we also evaluate CAC's recoverability from DNA storage errors. The result shows CAC is comparable to those of existing encoding schemes.
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DP-DNA: A Digital Pattern-Aware DNA Encoding Scheme to Improve Encoding Density of DNA Storage
With the rapid increase of available digital data, we are searching for a storage media with high density and capability of long-term preservation. Deoxyribonucleic Acid (DNA) storage is identified as such a promising candidate, especially for archival storage systems. However, the encoding density (i.e., how many binary bits can be encoded into one nucleotide) and error handling are two major factors intertwined in DNA storage. Considering encoding density, theoretically, one nucleotide (i.e., A, T, G, or C) can encode two binary bits (upper bound). However, due to biochemical constraints and other necessary information associated with payload, currently the encoding densities of various DNA storage systems are much less than this upper bound. Additionally, all existing studies of DNA encoding schemes are based on static analysis and really lack the awareness of dynamically changed digital patterns. Therefore, the gap between the static encoding and dynamic binary patterns prevents achieving a higher encoding density for DNA storage systems. In this paper, we propose a new Digital Pattern-Aware DNA storage system, called DP-DNA, which can efficiently store digital data in the DNA storage with high encoding density. DP-DNA maintains a set of encoding codes and uses a digital pattern-aware code (DPAC) to analyze the patterns of a binary sequence for a DNA strand and selects an appropriate code for encoding the binary sequence to achieve a high encoding density. An additional encoding field is added to the DNA encoding format, which can distinguish the encoding scheme used for those DNA strands, and thus we can decode DNA data back to its original digital data. Moreover, to further improve the encoding density, a variable-length scheme is proposed to increase the feasibility of the code scheme with a high encoding density. Finally, the experimental results indicate that the proposed DP-DNA achieves up to 103.5% higher encoding densities than prior work.
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- Award ID(s):
- 2204656
- PAR ID:
- 10500537
- Publisher / Repository:
- IEEE
- Date Published:
- ISBN:
- 979-8-3503-1948-4
- Page Range / eLocation ID:
- 1 to 8
- Format(s):
- Medium: X
- Location:
- Stony Brook, NY, USA
- Sponsoring Org:
- National Science Foundation
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