Computational applications of DNA physical scales

Pierre Baldi, Yves Chauvin, Søren Brunak, Jan Gorodkin, Anders Gorm Pedersen

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review


    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.
    Original languageEnglish
    Title of host publicationProceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology
    Place of PublicationMenlo Park
    PublisherAAAI Press
    Publication date1998
    Publication statusPublished - 1998
    EventSixth International Conference on Intelligent Systems for Molecular Biology - Montreal, Canada
    Duration: 28 Jun 19981 Jul 1998
    Conference number: 6


    ConferenceSixth International Conference on Intelligent Systems for Molecular Biology
    Internet address


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