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DNA storage code[1]

Description

Code that was designed (or that can be applied) to encode information into the four-base-pair alphabet of a DNA molecule.

There exist several proposals tailored specifically for DNA storage [1–5].

Protection

Noise affecting DNA molecules can include insertions and deletions [6]. The DNA data storage channel has been characterized [1,6,7].

Notes

Review of DNA-based coding [8].

Cousins

Member of code lists

Primary Hierarchy

Classical Domain
Galois-field Kingdom
\(q\)-ary codeECC
Editing code
Parents
Editing code
DNA codes can typically handle base-pair insertions and deletions.
DNA storage code
Children
Fountain code
Fountain codes have been used for DNA storage [11].

References

[1]
H. M. Kiah, G. J. Puleo, and O. Milenkovic, “Codes for DNA Storage Channels”, (2015) arXiv:1410.8837
[2]
S. M. H. T. Yazdi, Y. Yuan, J. Ma, H. Zhao, and O. Milenkovic, “A Rewritable, Random-Access DNA-Based Storage System”, (2015) arXiv:1505.02199
[3]
S. M. H. T. Yazdi, R. Gabrys, and O. Milenkovic, “Portable and Error-Free DNA-Based Data Storage”, Scientific Reports 7, (2017) DOI
[4]
W. H. Press, J. A. Hawkins, S. K. Jones Jr, J. M. Schaub, and I. J. Finkelstein, “HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints”, Proceedings of the National Academy of Sciences 117, 18489 (2020) DOI
[5]
T. T. Nguyen, K. Cai, K. A. Schouhamer Immink, and H. M. Kiah, “Capacity-Approaching Constrained Codes With Error Correction for DNA-Based Data Storage”, IEEE Transactions on Information Theory 67, 5602 (2021) DOI
[6]
R. Heckel, G. Mikutis, and R. N. Grass, “A Characterization of the DNA Data Storage Channel”, (2018) arXiv:1803.03322
[7]
H. M. Kiah, G. J. Puleo, and O. Milenkovic, “Codes for DNA Sequence Profiles”, (2015) arXiv:1502.00517
[8]
S. M. H. T. Yazdi, H. M. Kiah, E. R. Garcia, J. Ma, H. Zhao, and O. Milenkovic, “DNA-Based Storage: Trends and Methods”, (2015) arXiv:1507.01611
[9]
X. Lu, J. Jeong, J.-W. Kim, J.-S. No, H. Park, A. No, and S. Kim, “Error Rate-Based Log-Likelihood Ratio Processing for Low-Density Parity-Check Codes in DNA Storage”, IEEE Access 8, 162892 (2020) DOI
[10]
R. N. Grass, R. Heckel, M. Puddu, D. Paunescu, and W. J. Stark, “Robust Chemical Preservation of Digital Information on DNA in Silica with Error‐Correcting Codes”, Angewandte Chemie International Edition 54, 2552 (2015) DOI
[11]
Y. Erlich and D. Zielinski, “DNA Fountain enables a robust and efficient storage architecture”, Science 355, 950 (2017) DOI
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Zoo Code ID: dna

Cite as:
“DNA storage code”, The Error Correction Zoo (V. V. Albert & P. Faist, eds.), 2022. https://errorcorrectionzoo.org/c/dna
BibTeX:
@incollection{eczoo_dna, title={DNA storage code}, booktitle={The Error Correction Zoo}, year={2022}, editor={Albert, Victor V. and Faist, Philippe}, url={https://errorcorrectionzoo.org/c/dna} }
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Permanent link:
https://errorcorrectionzoo.org/c/dna

Cite as:

“DNA storage code”, The Error Correction Zoo (V. V. Albert & P. Faist, eds.), 2022. https://errorcorrectionzoo.org/c/dna

Github: https://github.com/errorcorrectionzoo/eczoo_data/edit/main/codes/classical/q-ary_digits/alternative_metrics/insertion_deletion/dna.yml.