Repetition Coding as an Effective Error Correction Code for Information Encoded in DNA

Haughton, David; Balado, Félix

doi:10.1109/bibe.2011.45

Cited by 11 publications

(13 citation statements)

References 13 publications

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“…Resynchronisation was performed using the heuristic multiple sequence alignment algorithm MUSCLE, followed by majority decoding on the aligned sequences. This resynchronisation procedure was previously proposed by us [22], however unlike here, it did not operate under the no-start-codon constraint. Figure 3 shows the mutual information of the watermark codes in addition to the bound presented in Section 4 and a bound proposed in prior work [20].…”

Section: Resultsmentioning

confidence: 94%

A modified watermark synchronisation code for robust embedding of data in DNA

Haughton

Balado

2013

2013 IEEE International Conference on Acoustics, Speech and Signal Processing

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Section: Resultsmentioning

confidence: 94%

A modified watermark synchronisation code for robust embedding of data in DNA

Haughton

Balado

2013

2013 IEEE International Conference on Acoustics, Speech and Signal Processing

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“…The parameters used in the cascaded Kimura model are q =10 −8 and γ =0.1, which are values used in prior work [7] and are based on realistic estimates obtained in [28]. The results for BioCode ncDNA were obtained using messages of length 10,000 bits.…”

Section: Resultsmentioning

confidence: 99%

“…This model becomes the less realistic Jukes-Cantor model when γ =1. For a more in-depth explanation the reader is directed to [7]. …”

Section: Methodsmentioning

confidence: 99%

“…Stored information is passed from generation to generation when placed anywhere in the genome of asexual organisms. Data encoded in DNA is subject to errors caused by random mutations in the organism’s DNA, but if encoded correctly it may still be retrievable after millions of generations or more [7]. Encoding information in sexually reproducing organisms is more complicated due to the effects of genetic crossover.…”

Section: Introductionmentioning

confidence: 99%

“…Also included was an in silico analysis of their method, showing the data recovery rate for a varying mutation rate. This work was expanded upon by Haughton and Balado [7]. …”

Section: Introductionmentioning

confidence: 99%

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BioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA

Haughton

Balado

2013

BMC Bioinformatics

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BackgroundIn recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA. Inherently DNA is a digital medium whereby the nucleotide bases act as digital symbols, a fact which underpins all bioinformatics techniques, and which also makes trivial information encoding using DNA straightforward. However, the situation is more complex in methods which aim at embedding information in the genomes of living organisms. DNA is susceptible to mutations, which act as a noisy channel from the point of view of information encoded using DNA. This means that the DNA data embedding field is closely related to digital communications. Moreover it is a particularly unique digital communications area, because important biological constraints must be observed by all methods. Many DNA data embedding algorithms have been presented to date, all of which operate in one of two regions: non-coding DNA (ncDNA) or protein-coding DNA (pcDNA).ResultsThis paper proposes two novel DNA data embedding algorithms jointly called BioCode, which operate in ncDNA and pcDNA, respectively, and which comply fully with stricter biological restrictions. Existing methods comply with some elementary biological constraints, such as preserving protein translation in pcDNA. However there exist further biological restrictions which no DNA data embedding methods to date account for. Observing these constraints is key to increasing the biocompatibility and in turn, the robustness of information encoded in DNA.ConclusionThe algorithms encode information in near optimal ways from a coding point of view, as we demonstrate by means of theoretical and empirical (in silico) analyses. Also, they are shown to encode information in a robust way, such that mutations have isolated effects. Furthermore, the preservation of codon statistics, while achieving a near-optimum embedding rate, implies that BioCode pcDNA is also a near-optimum first-order steganographic method.

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Sector‐based DNA information hiding method

Santoso

Lee

Hwang

et al. 2016

Security Comm Networks

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As the next generation sequencing and deoxyribonucleic acid (DNA) synthesis technologies rapidly develop, DNA engineering became faster and cheaper with higher accuracy than before. External information such as secret messages or digital archives can be embedded into the DNA sequence by mutating its molecular sequence according to a certain algorithm. This study presents a sector‐based DNA steganography method using non‐coding regions of the DNA sequence as the host for carrying binary data. The aim of the sector‐based embedding is to have a high level of security, data capacity, and error handling while preserving the organism's life information. A sector consists of reference bases, segmented message bases, and parity bases. The parity bases can detect and handle mutation errors in each sector. The sector length controls the data capacity and security. Our in silico experiments verified that the bit‐per‐nucleotide of our method can be [1.2, 2.0] by controlling the sector length, which is 0.2 point higher than that of conventional methods. As many as 104 base mutations in the DNA sequence can be handled for perfect message retrieval. Furthermore, the probability for message detection without keys is lower than 1.3949 × 10−62, which is very low. Copyright © 2016 John Wiley & Sons, Ltd.

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Repetition Coding as an Effective Error Correction Code for Information Encoded in DNA

Cited by 11 publications

References 13 publications

A modified watermark synchronisation code for robust embedding of data in DNA

A modified watermark synchronisation code for robust embedding of data in DNA

BioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA

Sector‐based DNA information hiding method

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