Codes for DNA storage channels

Han Mao Kiah, Gregory J. Puleo, Olgica Milenkovic

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

Abstract

We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. This problem of reconstructing sequences from traces was first investigated in the noiseless setting under the name of "Markov type" analysis. Here, we explain the connection between the problem and the problem of DNA synthesis and sequencing, and introduce the notion of a DNA storage channel. We analyze the number of sequence equivalence classes under the channel mapping and propose new asymmetric coding techniques to combat the effects of synthesis noise. In our analysis, we make use of Ehrhart theory for rational polytopes.

Original languageEnglish (US)
Title of host publication2015 IEEE Information Theory Workshop, ITW 2015
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781479955268
DOIs
StatePublished - Jun 24 2015
Event2015 IEEE Information Theory Workshop, ITW 2015 - Jerusalem, Israel
Duration: Apr 26 2015May 1 2015

Publication series

Name2015 IEEE Information Theory Workshop, ITW 2015

Other

Other2015 IEEE Information Theory Workshop, ITW 2015
CountryIsrael
CityJerusalem
Period4/26/155/1/15

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Networks and Communications
  • Information Systems
  • Computational Theory and Mathematics

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