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1998

Computational Applications of DNA Structural Scales

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Computational Applications of DNA Structural Scales
We study from a computational standpoint several different physicalscales associatedwith structural features of DNA sequences, including dinucleotide scales such as base stacking energy and propeller 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 promoter 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 therefore complement each other.
Pierre Baldi, Søren Brunak, Yves Chauvin, A
Added 01 Nov 2010
Updated 01 Nov 2010
Type Conference
Year 1998
Where ISMB
Authors Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
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