Hairpin Structures in DNA Words

  title={Hairpin Structures in DNA Words},
  author={Lila Kari and Stavros Konstantinidis and Elena Losseva and Petr Sos{\'i}k and Gabriel Thierrin},
We formalize the notion of a DNA hairpin secondary structure, examining its mathematical properties. Two related secondary structures are also investigated, taking into the account imperfect bonds (bulges, mismatches) and multiple hairpins. We characterize maximal sets of hairpin-forming DNA sequences, as well as hairpin-free ones. We study their algebraic properties and their computational complexity. Related polynomial-time algorithms deciding hairpin-freedom of regular sets are presented… CONTINUE READING

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