Easy Promoter Prediction Program (EP3)Conversion tables
EP3 uses conversion tables retrieved from the literature to convert the nucleotide sequence into a profile. These conversion tables can be downloaded here. Below is a brief description of each of the properties along with a reference to the literature. When using this compilation, please cite the paper. The EP3 program only uses the best performing encoding (Base stacking energy) as detailed in the paper. The other properties are shown here for those interested.
- Stacking Energy
- Dinucleotide base stacking energy represents how easily parts of the DNA de-stack. A high peak for this value represents an unstable region while a low peak represents more stable region. Ornstein 1978
- Propeller twist
- The dinucleotide propeller twist is the value for the flexibility of the helix. Low values indicate flexible areas whereas high values indicate rigid areas. El Hassan, 1996
- Nucleosome Position Preference
- NPP is a trinucleotide model that calculates the unlikeliness of the sequence being within a nucleosome. High values represent regions with a lower likelihood of nucleosome appearance. Satchwell 1986
- Bendability
- The trinucleotide bendability model models the bendability of the DNA towards the major groove. Sections with high values are more bendable than regions with a low value. Brukner 1995
- A-philicity
- A region in the DNA with a high A-philicity value is more easily converted to the A-form than a low value region, which is more resistant to transition. Ivanov 1994
- Protein Induced Deformability
- With this property a larger value reflects a more deformable sequence while a smaller value indicates a region where the DNA helix is less likely to be changed dramatically by proteins. Olson 1998
- Duplex Stability Disrupt Energy
- Regions with a high disrupt energy value will be more stable than regions with a lower energy value. Breslauer 1986
- Duplex Stability Free Energy
- Regions with low free energy content will be more stable than regions with high thermodynamic energy content. Sugimoto 1996
- DNA denaturation
- DNA regions with a low value are more likely to denaturate than regions with a higher value. Blake 1998, Blake 1999
- DNA Bending stiffness
- High values correspond to DNA regions that are more rigid, while low values correspond to regions that will bend more easily. Sivolob 1995
- B-DNA twist
- Structures with a low twist region appear to unwind in response to steric clashes of large exocylic groups in the major and minor grooves and those with high twist values are subject to lesser contact. Gorin 1995
- Protein-DNA twist
- High peak values are more likely to be deformed by proteins than regions with a lower peak value. Olson 1998
- Stabilizing energy of Z-DNA
- Stretches of DNA with low values are more likely to form Z-DNA than a high-value region. Ho 1990
