RNA_Structure_Visualizer

RNA secondary structure predictor based on the Nussinov algorithm that generates all optimal structures utilizing the Wuchty algorithm with visualization of the best predicted secondary structure.

Installation

Run the program through the terminal

1. Clone the repo
2. Install the neccessary libaries (tqdm, networkx, plotly, matplotlib, and nbformat)

pip3 install tqdm
pip3 install networkx
pip3 install plotly
pip3 install matplotlib
pip3 install nbformat 

Run the program interactively through a Jupyter notebook

1. Clone the repo
2. Run each code within the Jupyter notebook sequentially

Usage (Terminal version)

--ref <[0, 7]>      Test/reference sequences from RNA Central and RFam database (0-7)
--seq SEQUENCE      RNA sequence
--struct STRUCTURE  RNA structure in dot-parenthesis notation wrapped in quotes
--limit LIMIT       Limit on the number of optimal solutions to return (smaller numbers run faster and won't crash due to memory usage
--vis               Flag to visualize the best predicted structure

Example

Utilize reference sequence from RFam database from RNA Central

python3 nussinov.py --ref 0

ID: URS00006B0FB5_357808
Generated 1540 optimal structures.
100%|████████████████████████████████████████████████████████████████████████████████████████| 1540/1540 [00:00<00:00, 329065.57it/s]
Best predicted structure accuracy: 0.7
Average predicted structure accuracy: 0.14894241040344977
Best structure: (.().(((((((..()))))))))

Use your own sequence and reference structure

python3 nussinov.py --seq AUGG --struct "().."

Generated 1 optimal structures.
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 19599.55it/s]
Best predicted structure accuracy: 1.0
Average predicted structure accuracy: 1.0
Best structure: ()..