Implementation of the Zuker algorithm for the RNA folding problem.
RNA folding is the process by which a linear ribonucleic acid (RNA) molecule acquires secondary structure through intra-molecular interactions. The folded domains of RNA molecules are often the sites of specific interactions with proteins in forming RNA–protein (ribonucleoprotein) complexes.
Please make sure that you have Python 3.8.3 or greater installed on your machine. It is also possible that the code will run for previous versions (not tested).
Also make sure that the following libraries are installed and up-to-date:
- numpy
- matplotlib
- importlib
In addition, the draw_rna visualization tool was utilized. draw_rna was developed the Das Lab and can be found here. A tweaked version of its draw.py script is utilized in the frame of this implementation -included in the src directory- as well as the draw_struct function which is proposed by draw_rna for RNA secondary structure visualization.
The Jupyter notebook is fairly easy to run; it includes the implementation of the Zuker algorithm as well as the assumptions made in the toy problem.