Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage

Xie, Ranze; Zan, Xiangzhen; Chu, Ling; Su, Yanqing; Xu, Peng; Liu, Wenbin

doi:10.1186/s12859-023-05237-9

Cited by 12 publications

(4 citation statements)

References 31 publications

(42 reference statements)

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“…Meiser et al ( 2020) have used a Reed-Solomon code for storing a full album of music in DNA [33]. Recently, Xie et al ( 2023) conducted an analysis showing the value of the sequencing depth for retrieving the right string of data [34]. Sufficiently deep sequencing allows the use of MSA (multiple sequence alignment) methods to establish a consensus sequence and correct errors that may appear on the DNA strands.…”

Section: New Storage Medium Old Problems and Solutionsmentioning

confidence: 99%

DNA Data Storage

Buko,

Tuczko,

Ishikawa

2023

BioTech

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The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage.

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Section: New Storage Medium Old Problems and Solutionsmentioning

confidence: 99%

DNA Data Storage

Buko,

Tuczko,

Ishikawa

2023

BioTech

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“…A further approach is the exploitation of sequencing depth by using a form of majority voting for sequencing reads, which allows compensation for indels that occurred during sequencing. 14 The DNA data storage channel consists of multiple steps, the writing of data into DNA (synthesis), the amplification of the synthesis product using PCR, the storage process itself, and the reading of the DNA back into a digital format (sequencing). Each component, including the various options for a component (for example, different sequencing machines), exhibits unique error profiles and error patterns.…”

Section: Introductionmentioning

confidence: 99%

Turbo autoencoders for the DNA data storage channel with Autoturbo-DNA

Welzel,

Dreßler,

Heider

2024

iScience

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“…Synthetic DNA has now been proved to be a new potential storage medium for exponentially growing data. , The total amount of data stored in synthetic DNA has reached the GB level; various practical automated read/write technologies for DNA storage have been proposed. − Unlike traditional electric/optical/magnetic storage media, DNA storage is characterized by a large amount of insertions, deletions, and substitutions (IDSs) due to highly error-prone DNA synthesis and sequencing processes . The difficulty of data recovery mainly comes from the synchronization problem because of random insertions and deletions.…”

Section: Introductionmentioning

confidence: 99%

A Robust and Efficient DNA Storage Architecture Based on Modulation Encoding and Decoding

Zan

Xie

Yao

et al. 2023

J. Chem. Inf. Model.

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Synthetic DNA has been widely considered an attractive medium for digital data storage. However, the random insertion−deletion−substitution (IDS) errors in the sequenced reads still remain a critical challenge to reliable data recovery. Motivated by the modulation technique in the communication field, we propose a new DNA storage architecture to solve this problem. The main idea is that all binary data are modulated into DNA sequences with the same AT/GC patterns, which facilitate the detection of indels in noisy reads. The modulation signal could not only satisfy the encoding constraints but also serve as prior information to detect the potential positions of errors. Experiments on simulation and real data sets demonstrate that modulation encoding provides a simple way to comply with biological constraints for sequence encoding (i.e., balanced GC content and avoiding homopolymers). Furthermore, modulation decoding is highly efficient and extremely robust, which can correct up to ∼40% of errors. In addition, it is robust to imperfect clustering reconstruction, which is very common in practice. Although our method has a relatively low logical density of 1.0 bits/nt, its high robustness may provide a wide space for developing low-cost synthetic technologies. We believe this new architecture may boost the early coming of large-scale DNA storage applications in the future.

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Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage

Cited by 12 publications

References 31 publications

DNA Data Storage

DNA Data Storage

Turbo autoencoders for the DNA data storage channel with Autoturbo-DNA

A Robust and Efficient DNA Storage Architecture Based on Modulation Encoding and Decoding

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