Rank-modulation codes for DNA storage with shotgun sequencing

Netanel Raviv, Moshe Schwartz, Eitan Yaakobi

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


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. Furthermore, a technique for deciding the feasibility of a permutation is devised. By using insights from 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
Article number8347019
Pages (from-to)50-64
Number of pages15
JournalIEEE Transactions on Information Theory
Issue number1
StatePublished - 1 Jan 2019


  • DNA storage
  • DeBruijn graphs
  • permutations codes

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Library and Information Sciences


Dive into the research topics of 'Rank-modulation codes for DNA storage with shotgun sequencing'. Together they form a unique fingerprint.

Cite this