DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage

Abstract DNA storage is one of the most promising ways for future information storage due to its high data storage density, durable storage time and low maintenance cost. However, errors are inevitable during synthesizing, storing and sequencing. Currently, many error correction algorithms have been...

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Vydáno v:Briefings in bioinformatics Ročník 25; číslo 3
Hlavní autoři: Li, Yiming, Zhang, Haoling, Chen, Yuxin, Shen, Yue, Ping, Zhi
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 27.03.2024
Oxford Publishing Limited (England)
Témata:
Algorithms
Codec
Contamination
Data analysis
Data storage
Data structures
Density
Deoxyribonucleic acid
DNA
DNA biosynthesis
DNA structure
Error correction
Gene sequencing
Information processing
Information retrieval
Information storage
Maintenance costs
Nucleotide sequence
Problem Solving Protocol
Version control
anti-contamination
DNA-based data storage
bloom filter
file version control
ISSN:1467-5463, 1477-4054, 1477-4054
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Shrnutí:Abstract DNA storage is one of the most promising ways for future information storage due to its high data storage density, durable storage time and low maintenance cost. However, errors are inevitable during synthesizing, storing and sequencing. Currently, many error correction algorithms have been developed to ensure accurate information retrieval, but they will decrease storage density or increase computing complexity. Here, we apply the Bloom Filter, a space-efficient probabilistic data structure, to DNA storage to achieve the anti-error, or anti-contamination function. This method only needs the original correct DNA sequences (referred to as target sequences) to produce a corresponding data structure, which will filter out almost all the incorrect sequences (referred to as non-target sequences) during sequencing data analysis. Experimental results demonstrate the universal and efficient filtering capabilities of our method. Furthermore, we employ the Counting Bloom Filter to achieve the file version control function, which significantly reduces synthesis costs when modifying DNA-form files. To achieve cost-efficient file version control function, a modified system based on yin–yang codec is developed.
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ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbae125