Respiratory for the prediction of RNA 2D structure using integer programming.
RNA2DPred is a Python-based program to predict RNA secondary structure using either energy-based method (MFE), probability-based method (MEA), pattern matching method or 2 of them together (bi-objective optimization).
The main file for structure prediction is RNA2DPred.py, but the other file motif_alignment.py can be run independently as an alignment tool.
- ViennaRNA package, which its instruction of installation is here: https://www.tbi.univie.ac.at/RNA/#download
- IBM ILOG CPLEX Optimization Studio, which can be downloaded using academic email address here: https://www.ibm.com/products/ilog-cplex-optimization-studio
The usage of program motif_alignment.py is like below:
python3 motif_alignment.py --sequence [sequence filename]/[sequence] --motif [motif filename]/[motif sequence] --identity [0 - 1] --format [0,1] --output [output filename] --verbose
Run python3 motif_alignment.py --help for more details.
The usage of program RNA2DPred.py is like below:
python3 RNA2DPred.py --sequence [sequence filename]/[sequence] --motif [motif filename] --identity [0 - 1] --format [0,1] --output [output filename] --verbose
Run python3 RNA2DPred.py --help for more details.