Computational applications of DNA structural scales

Studies several different physical scales associated with the structural features of DNA sequences from a computational standpoint, 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 combination 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.