Embracing errors is more effective than avoiding them through constrained coding for DNA data storage

Franziska Weindel, Andreas L. Gimpel, Robert N. Grass, Reinhard Heckel

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the number of errors, a common technique is to include constraints that avoid homopolymers (consecutive repeated nucleotides) and balance the GC content, as sequences with homopolymers and unbalanced GC contents are often associated with larger error rates. However, constrained coding comes at the cost of an increase in redundancy. An alternative is to control the errors by randomizing the sequences, embracing the extra errors, and paying for them with additional coding redundancy. In this paper, we determine the error regimes in which embracing errors is more efficient than constrained coding. We find that constrained coding is inefficient in most common error regimes for DNA data storage. Specifically, the error probabilities for homopolymers and unbalanced GC contents must be very large for constrained coding to achieve a higher code rate than unconstrained coding.

Original languageEnglish
Title of host publication2023 59th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2023
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9798350328141
DOIs
StatePublished - 2023
Event59th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2023 - Monticello, United States
Duration: 26 Sep 202329 Sep 2023

Publication series

Name2023 59th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2023

Conference

Conference59th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2023
Country/TerritoryUnited States
CityMonticello
Period26/09/2329/09/23

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