Rank modulation codes for DNA storage

Netanel Raviv, Moshe Schwartz, Eitan Yaakobi

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

2 Scopus citations

Abstract

Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to maintain reliability in reading and writing, new coding schemes must be developed. In a reading technique called shotgun sequencing, a long DNA string is read in a sliding window fashion, and a profile vector is produced. It was recently suggested by Kiah et al. that such a vector can represent the permutation which is induced by its entries, and hence a rank modulation scheme arises. Although this interpretation suggests high error tolerance, it is unclear which permutations are feasible, and how to produce a DNA string whose profile vector induces a given permutation. In this paper, by observing some necessary conditions, an upper bound for the number of feasible permutations is given. Further, a technique for deciding the feasibility of a permutation is devised. By using this technique, an algorithm for producing a considerable number of feasible permutations is given, which applies to any alphabet size and any window length.

Original languageEnglish
Title of host publication2017 IEEE International Symposium on Information Theory, ISIT 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages3125-3129
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

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Information Systems
  • Modeling and Simulation
  • Applied Mathematics

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