Deterministic polynomial-time algorithms for designing short DNA words

Ming-Yang Kao, Henry C.M. Leung, He Sun*, Yong Zhang

*Corresponding author for this work

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

1 Scopus citations

Abstract

Designing short DNA words is a problem of constructing n DNA strings (words) with the minimum length such that the Hamming distance between each pair is at least k and the words satisfy a set of extra constraints. This problem has applications in DNA computing, DNA self-assembly, and DNA arrays. Previous works include those that extended results from coding theory to obtain bounds on code size for biologically motivated constraints and those that applied heuristic local searches, genetic algorithms, and randomized algorithms. In particular, Kao, Sanghi and Schweller developed polynomial-time randomized algorithms to construct n DNA words of length 9· max {logn,k} satisfying a sets of constraints with high probability. In this paper, we give deterministic polynomial-time algorithms to construct DNA words based on expander codes, Ramanujan graphs, and derandomization techniques. Our algorithms can construct n DNA words of length max {3logn, 4k} or 2.1 logn + 6.28 k satisfying the same sets of constraints as the words constructed by the algorithms of Kao et al. We have also extended these algorithms to construct words that satisfy a larger set of constraints for which the algorithms of Kao et al. do not work.

Original languageEnglish (US)
Title of host publicationTheory and Applications of Models of Computation - 7th Annual Conference, TAMC 2010, Proceedings
PublisherSpringer Verlag
Pages308-319
Number of pages12
ISBN (Print)3642135617, 9783642135613
DOIs
StatePublished - Jan 1 2010
Event7th Annual Conference on Theory and Applications of Models of Computation, TAMC 2010 - Prague, Czech Republic
Duration: Jun 7 2010Jun 11 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6108 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other7th Annual Conference on Theory and Applications of Models of Computation, TAMC 2010
CountryCzech Republic
CityPrague
Period6/7/106/11/10

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Keywords

  • DNA computating
  • DNA words design
  • Ramanujan graphs
  • coding theory
  • derandomization
  • expander codes

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Kao, M-Y., Leung, H. C. M., Sun, H., & Zhang, Y. (2010). Deterministic polynomial-time algorithms for designing short DNA words. In Theory and Applications of Models of Computation - 7th Annual Conference, TAMC 2010, Proceedings (pp. 308-319). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6108 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-642-13562-0_28