Abstract
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 language | English |
|---|---|
| Title of host publication | Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology |
| Place of Publication | Menlo Park |
| Publisher | AAAI Press |
| Publication date | 1998 |
| Pages | 35-42 |
| Publication status | Published - 1998 |
| Event | Sixth International Conference on Intelligent Systems for Molecular Biology - Montreal, Canada Duration: 28 Jun 1998 → 1 Jul 1998 Conference number: 6 https://web.archive.org/web/20140223112627/http://www-lbit.iro.umontreal.ca/ISMB98/ |
Conference
| Conference | Sixth International Conference on Intelligent Systems for Molecular Biology |
|---|---|
| Number | 6 |
| Country/Territory | Canada |
| City | Montreal |
| Period | 28/06/1998 → 01/07/1998 |
| Internet address |