An improved Huffman coding method for archiving text, images, and music characters in DNA

Ailenberg, Menachem; Rotstein, Ori D.

doi:10.2144/000113218

Cited by 66 publications

(46 citation statements)

References 11 publications

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“…The potential of DNA has been realized for various information-theoretic protocols, including DNA steganography for the identification of genetically modified organisms [12,21,23] hiding of messages in DNA [9,11,16,20] and long-term data storage in DNA [3,7,8,10,14,21]. These applications require mechanisms to validate, ensure, and possibly verify message accuracy.…”

Section: Introductionmentioning

confidence: 99%

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Improving Dependability and Precision of Data Encoding in DNA

Mueller¹,

Jafari²,

Roth³

2018

Eur J Exp Bio

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DNA storage of information is emerging as the next-generation approach to archiving vast amounts of data. Various sophisticated approaches for data storage in DNA have been proposed. Herein we present a multistep algorithm designed to detect and/or correct errors introduced at any stage of the DNA storage process, including those during message DNA generation, and propose refinements designed to ensure authenticity and correctness of each individual encoded DNA block. In addition, the algorithm allows authentic decoding without a reference sequence or message meaning. The algorithm is designed based on principles underlying provably secure cryptographic systems. Importantly, our new algorithm compares favorably with current ones in terms of ease of implementation and message expansion. In cases where reads are error-free, our algorithm should be faster than current alignment techniques. Without knowing the original data, a certificate is generated that confirms that the obtained data are exactly the same as the original. Our algorithm has applications to DNA steganography, sequence alignment, fast identification of correct reads in next generation sequencing and to message security.

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Section: Introductionmentioning

confidence: 99%

“…3 , where i 3 is the base-3 representation of i, prepended with zeros so that ID i is of fixed length l id : The difference to above is that k 1's are inserted in each identifier. This special structure will be used during a verification step during decoding.…”

mentioning

confidence: 99%

Improving Dependability and Precision of Data Encoding in DNA

Mueller¹,

Jafari²,

Roth³

2018

Eur J Exp Bio

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show abstract

“…Advancement in using DNA as an information storage medium continues, both experimentally (Pak Chung Wong, 2003; Kashiwamura et al, 2005; Yachie et al, 2007) and algorithmically (Ailenberg and Rotstein, 2009). Yet, practical and large-scale implementation remains unfavorable due to technological limitations on robust DNA synthesis and sequencing technology.…”

Section: Introductionmentioning

confidence: 99%

The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module

Yim

et al. 2014

Front. Bioeng. Biotechnol.

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The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms – short synthesized DNA fragments without homopolymer. Here, we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g., algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with low-density parity-check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programing framework – DNAcodec with an eXtensible Markup Language-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error tolerance, which opens the field to biocomputing and synthetic biology.

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“…Ailenberg and Rotstein [8] have developed a coding scheme to encode an image that is composed of shapes and their coordinates.…”

Section: Insertion Of Media Other Than Textmentioning

confidence: 99%

“…Steganography with a number of papers having been published in the last two decades [1][2][3][4][5][6][7][8][9][10][11][12][13].…”

mentioning

confidence: 99%

A forensics software toolkit for DNA steganalysis.

Beck

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An improved Huffman coding method for archiving text, images, and music characters in DNA

Cited by 66 publications

References 11 publications

Improving Dependability and Precision of Data Encoding in DNA

Improving Dependability and Precision of Data Encoding in DNA

The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module

A forensics software toolkit for DNA steganalysis.

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