Repeat-Free Codes

Ohad Elishco, Ryan Gabrys, Eitan Yaakobi, Muriel Medard

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

In this paper we consider the problem of encoding data into repeat-free sequences in which sequences are imposed to contain any k -tuple at most once (for predefined k ). First, the capacity of the repeat-free constraint are calculated. Then, an efficient algorithm, which uses two bits of redundancy, is presented to encode length- n sequences for k=2+2log (n). This algorithm is then improved to support any value of k of the form k=alog (n) , for 1< a , while its redundancy is o(n). We also calculate the capacity of repeat-free sequences when combined with local constraints which are given by a constrained system, and the capacity of multi-dimensional repeat-free codes.

Original languageEnglish
Article number9465135
Pages (from-to)5749-5764
Number of pages16
JournalIEEE Transactions on Information Theory
Volume67
Issue number9
DOIs
StatePublished - 1 Sep 2021

Keywords

  • DNA sequences
  • Information theory
  • capacity
  • constrained coding
  • encoder construction
  • error-correcting codes

ASJC Scopus subject areas

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

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