The DegScore model is a ridge regression trained on Eterna Roll-Your-Own structure data to predict RNA degradation.
Citation: Leppek, K., Byeon, G.W., Kladwang, W., Wayment-Steele, H.K., Kerr, C., ... Barna, M., Das, R. (2021). Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. https://www.biorxiv.org/content/10.1101/2021.03.29.437587v1.
If you find this code useful, please cite
Wayment-Steele, H., Kim., D.S. DegScore. (2022) Zenodo. https://doi.org/10.5281/zenodo.7130659
Add to python path in .bashrc, or in python code with
sys.path.append('/path/to/DegScore')
Example syntax:
from DegScore import DegScore
mdl = DegScore('GGGUUUCCC', structure='(((...)))')
print(mdl.degscore_by_position)
print(mdl.degscore)
print(mdl.est_half_life)
Output:
[0.17 0.217 0.511 0.641 0.714 0.49 0.347 0.15 0.643]
3.8830000000000013
11.430771365678682
| Experiment | Data Repository |
|---|---|
| pH 10, Mg2+=10 mM, 24˚C, 1 day | https://rmdb.stanford.edu/detail/RYOS1_MGPH_0000 |
| pH 10, Mg2+=0 mM, 24˚C, 7 days | https://rmdb.stanford.edu/detail/RYOS1_PH10_0000 |
| pH 7.2, Mg2+=10 mM, 50˚C, 1 day | https://rmdb.stanford.edu/detail/RYOS1_MG50_0000 |
| pH 7.2, Mg2+=0 mM, 50˚C, 7 days | https://rmdb.stanford.edu/detail/RYOS1_50C_0000 |
| SHAPE structure mapping | https://rmdb.stanford.edu/detail/SHAPE_RYOS_0620 |
Kaggle competition for degradation prediction, which used the same training/test dataset: https://www.kaggle.com/c/stanford-covid-vaccine
For more details on usage, and how degradation rate and half life are estimated from DegScore, see Demo/Degscore_demo.ipynb.
For code and data to reproduce a similar windowed Ridge regression model, see ReproduceDegscore/reproduce_degscore.ipynb. (Note fit is stochastic so coefficients cannot be reproduced exactly.)
If a secondary structure is not provided and Arnie is set up, DegScore can also calculate a secondary structure in place.
The default package is set to EternaFold, to be the same as the Eterna DegScore 2.1 calculation. This requires having successfully set up Arnie with EternaFold.
To change to other Arnie settings:
To use ViennaRNA (if set up):
mdl = DegScore(sequence, package='vienna', linear=False)
To use LinearFold-V (if set up):
mdl = DegScore(sequence, package='vienna', linear=True)
