Achievable Rates of Concatenated Codes in DNA Storage under Substitution Errors

Andreas Lenz, Lorenz Welter, Sven Puchinger

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

6 Scopus citations

Abstract

In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many, short DNA strands. Second, the strands are stored in an unordered fashion inside the storage medium and each strand is replicated many times. Third, the data is accessed in an uncontrollable manner, i.e., random strands are drawn from the medium and received, possibly with errors. As one of our results, we show that there is a significant gap between the channel capacity and the achievable rate of a standard concatenated code in which one strand corresponds to an inner block. This is in fact surprising as for other channels, such as q-ary symmetric channels, concatenated codes are known to achieve the capacity. We further propose a modifiedconcatenated coding scheme by combining several strands into one inner block, which allows to narrow the gap and achieve rates that are close to the capacity.

Original languageEnglish
Title of host publicationProceedings of 2020 International Symposium on Information Theory and its Applications, ISITA 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages269-273
Number of pages5
ISBN (Electronic)9784885523304
DOIs
StatePublished - 24 Oct 2020
Externally publishedYes
Event16th International Symposium on Information Theory and its Applications, ISITA 2020 - Virtual, Kapolei, United States
Duration: 24 Oct 202027 Oct 2020

Publication series

NameProceedings of 2020 International Symposium on Information Theory and its Applications, ISITA 2020

Conference

Conference16th International Symposium on Information Theory and its Applications, ISITA 2020
Country/TerritoryUnited States
CityVirtual, Kapolei
Period24/10/2027/10/20

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