Noise and uncertainty in string-duplication systems

Siddharth Jain, Farzad Farnoud, Moshe Schwartz, Jehoshua Bruck

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

10 Scopus citations

Abstract

Duplication mutations play a critical role in the generation of biological sequences. Simultaneously, they have a deleterious effect on data stored using in-vivo DNA data storage. While duplications have been studied both as a sequence-generation mechanism and in the context of error correction, for simplicity these studies have not taken into account the presence of other types of mutations. In this work, we consider the capacity of duplication mutations in the presence of point-mutation noise, and so quantify the generation power of these mutations. We show that if the number of point mutations is vanishingly small compared to the number of duplication mutations of a constant length, the generation capacity of these mutations is zero. However, if the number of point mutations increases to a constant fraction of the number of duplications, then the capacity is nonzero. Lower and upper bounds for this capacity are also presented. Another problem that we study is concerned with the mismatch between code design and channel in data storage in the DNA of living organisms with respect to duplication mutations. In this context, we consider the uncertainty of such a mismatched coding scheme measured as the maximum number of input codewords that can lead to the same output.

Original languageEnglish
Title of host publication2017 IEEE International Symposium on Information Theory, ISIT 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages3120-3124
Number of pages5
ISBN (Electronic)9781509040964
DOIs
StatePublished - 9 Aug 2017
Event2017 IEEE International Symposium on Information Theory, ISIT 2017 - Aachen, Germany
Duration: 25 Jun 201730 Jun 2017

Publication series

NameIEEE International Symposium on Information Theory - Proceedings
ISSN (Print)2157-8095

Conference

Conference2017 IEEE International Symposium on Information Theory, ISIT 2017
Country/TerritoryGermany
CityAachen
Period25/06/1730/06/17

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