A stitch in time: Efficient computation of genomic DNA melting bubbles

  title={A stitch in time: Efficient computation of genomic DNA melting bubbles},
  author={Eivind T{\o}stesen},
  journal={Algorithms for Molecular Biology : AMB},
  pages={10 - 10}
  • E. Tøstesen
  • Published 7 February 2008
  • Computer Science
  • Algorithms for Molecular Biology : AMB
BackgroundIt is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic.ResultsAn efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a… 

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