Codes for DNA sequence profiles

Han Mao Kiah, Gregory J. Puleo, Olgica Milenkovic

Research output: Chapter in Book/Report/Conference proceedingConference contribution


We consider the problem of storing information on synthetic DNA media and associated coding paradigms. The focal question of our analysis it how to construct and enumerate sequences that may be discriminated based on their collection of substrings observed through two types of noisy sequencing channels. In particular, we consider DNA sequences with balanced GC content, needed for chemical stability and desirable hybridization properties. We show that restricted de Bruijn graphs and Ehrhart theory for rational polytopes provide a suitable framework for studying such combinatorial questions.

Original languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Symposium on Information Theory, ISIT 2015
PublisherInstitute of Electrical and Electronics Engineers Inc.
Number of pages5
ISBN (Electronic)9781467377041
StatePublished - Sep 28 2015
EventIEEE International Symposium on Information Theory, ISIT 2015 - Hong Kong, Hong Kong
Duration: Jun 14 2015Jun 19 2015

Publication series

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


OtherIEEE International Symposium on Information Theory, ISIT 2015
Country/TerritoryHong Kong
CityHong Kong

ASJC Scopus subject areas

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


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