DNA storage code

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].Communicating with DNA may be simplified to a graph-based communication model [9].

Cousins

Low-density parity-check (LDPC) code— LDPC codes are potentially relevant for DNA storage [10].
Fountain code— Fountain codes have been used for DNA storage [11].
Simplex integer-based code— Simplex integer-based codewords are intended to model multisets of DNA molecules [12]. Points in a discrete simplex are in one-to-one correspondence to multisets because their coordinates denote the multiplicity of each element in a given multiset [12].
Reed-Solomon (RS) code— RS codes have been used for DNA storage [13].

Member of code lists

Classical codes

Primary Hierarchy

Classical Domain

Error-correcting code (ECC)

Block code

Editing code

Parents

Editing code

DNA codes can typically handle base-pair insertions and deletions.

DNA storage code

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]: Terlep, T. Arthur. A Mathematical Theory of Communication with Graphs and Symbols. Diss. Purdue University, 2024.
[10]: 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
[11]: Y. Erlich and D. Zielinski, “DNA Fountain enables a robust and efficient storage architecture”, Science 355, 950 (2017) DOI
[12]: M. Kovacevic and V. Y. F. Tan, “Codes in the Space of Multisets—Coding for Permutation Channels With Impairments”, IEEE Transactions on Information Theory 64, 5156 (2018) arXiv:1612.08837 DOI
[13]: 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

Page edit log

Victor V. Albert (2022-03-22) — most recent

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/properties/block/insertion_deletion/dna.yml.