Achievable Rates of Concatenated Codes in DNA Storage under Substitution Errors

Andreas Lenz, Lorenz Welter, Sven Puchinger

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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
PublisherIEEE
Publication date24 Oct 2020
Pages269-273
Article number9366092
ISBN (Electronic)9784885523304
Publication statusPublished - 24 Oct 2020
Event16th International Symposium on Information Theory and its Applications - Virtual, Kapolei, United States
Duration: 24 Oct 202027 Oct 2020
Conference number: 16

Conference

Conference16th International Symposium on Information Theory and its Applications
Number16
CountryUnited States
CityVirtual, Kapolei
Period24/10/202027/10/2020
SponsorResearch Society of Information Theory and its Applications, Engineering Sciences Society, IEICE
SeriesProceedings of 2020 International Symposium on Information Theory and its Applications, ISITA 2020

Bibliographical note

Funding Information:
This work has been supported by the European Union’s Horizon 2020 research and innovation programme under the the European Research Council (ERC) grant agreement no. 801434 and the Marie Sklodowska-Curie grant agreement no. 713683.

Publisher Copyright:
© 2020 IEICE.

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