Efficient and Explicit Balanced Primer Codes

Yeow Meng Chee, Han Mao Kiah, Hengjia Wei

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit constructions of error-correcting codes that are suitable as primer addresses and equip these constructions with efficient encoding algorithms. Specifically, our constructions take cyclic or linear codes as inputs and produce sets of primers with similar error-correcting capabilities. Using certain classes of BCH codes, we obtain infinite families of primer sets of length n , minimum distance d with (d+1) \log _{4}\,\,n +O(1) redundant symbols. Our techniques involve reversible cyclic codes (1964), an encoding method of Tavares et al. (1971) and Knuth's balancing technique (1986). In our investigation, we also construct efficient and explicit binary balanced error-correcting codes and codes for DNA computing.

Original languageEnglish
Article number9023377
Pages (from-to)5344-5357
Number of pages14
JournalIEEE Transactions on Information Theory
Volume66
Issue number9
DOIs
StatePublished - 1 Sep 2020

Keywords

  • Constrained coding
  • DNA-based data storage systems

ASJC Scopus subject areas

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

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