Randomized fast design of short DNA words

Ming-Yang Kao*, Manan Sanghi, Robert Schweller

*Corresponding author for this work

Research output: Contribution to journalConference articlepeer-review

6 Scopus citations


We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous work has extended results from coding theory to obtain bounds on code size for new biologically motivated constraints and has applied heuristic local search and genetic algorithm techniques for code design. This paper proposes a natural optimization formulation of the DNA code design problem in which the goal is to design n strings that satisfy a given set of constraints while minimizing the length of the strings. For multiple sets of constraints, we provide high-probability algorithms that run in time polynomial in n and any given constraint parameters, and output strings of length within a constant factor of the optimal. To the best of our knowledge, this work is the first to consider this type of optimization problem in the context of DNA code design.

Original languageEnglish (US)
Pages (from-to)1275-1286
Number of pages12
JournalLecture Notes in Computer Science
StatePublished - 2005
Event32nd International Colloquium on Automata, Languages and Programming, ICALP 2005 - Lisbon, Portugal
Duration: Jul 11 2005Jul 15 2005

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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