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Computational applications of DNA physical scales

  • Baldi, Pierre
  • Chauvin, Yves
  • Brunak, Søren
  • Gorodkin, Jan
  • Pedersen, Anders Gorm
Publication Date
Jan 01, 1998
Online Research Database In Technology
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The authors study from a computational standpoint several different physical scales associated with structural features of DNA sequences, including dinucleotide scales such as base stacking energy and propellor twist, and trinucleotide scales such as bendability and nucleosome positioning. We show that these scales provide an alternative or complementary compact representation of DNA sequences. As an example we construct a strand invariant representation of DNA sequences. The scales can also be used to analyze and discover new DNA structural patterns, especially in combinations with hidden Markov models (HMMs). The scales are applied to HMMs of human prmoter sequences revealing a number of significant differences between regions upstream and downstream of the transcriptional start point. Finally we show, with some qualifications, that such scales are by and large independent, and therfore complement each other.

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