Achieving the Capacity of the DNA Storage Channel

Andreas Lenz, Paul H. Siegel, Antonia Wachter-Zeh, Eitan Yaakohi

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

19 Scopus citations

Abstract

Significant advances in biochemical technologies, such as synthesizing and sequencing devices, have made DNA a competitive medium for archival data storage. In this paper we analyze storage systems based on these macromolecules from an information theoretic perspective. Using an appropriate channel model for the synthesis and sequencing steps, we study the maximum achievable information density per nucleotide for reliable and error resilient data storage. The channel model features the main attributes that characterize DNA-based data storage. That is, information is synthesized onto many short DNA strands, and each strand is copied many times. Due to the storage and sequencing methods, the receiver draws strands from these synthesized strands in an uncontrollable manner, where it is possible that strands are drawn multiple times and also that some strands are not drawn at all. Additionally, due to imperfections, the obtained strands can contain errors. Here we prove the achievability of a recently published upper bound on the Shannon capacity of this channel for a large range of parameters by proposing and analyzing a decoder that clusters received strands according to their similarity and then efficiently estimates the original strands based on these clusters.

Original languageEnglish
Title of host publication2020 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2020 - Proceedings
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages8846-8850
Number of pages5
ISBN (Electronic)9781509066315
DOIs
StatePublished - May 2020
Event2020 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2020 - Barcelona, Spain
Duration: 4 May 20208 May 2020

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
Volume2020-May
ISSN (Print)1520-6149

Conference

Conference2020 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2020
Country/TerritorySpain
CityBarcelona
Period4/05/208/05/20

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