The implementation of the paper "Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials".
Install PyTorch 1.6+, python 3.7+
- Clone the repo
git clone https://github.com/gongtiansu/KnotFold.git- Install python packages
cd KnotFold
pip install -r requirements.txt- KnotFold.py: predicting RNA secondary structure (bpseq format) from RNA sequence (fasta format).
python KnotFold.py -i <RNA_fasta> -o <output_dictionary> (--cuda)- KnotFold_mincostflow: constructing RNA secondary structure from base pairing probability using the minimum-cost flow algorithm.
KnotFold_mincostflow <prior_probability> <reference_probability> - KnotFold_mincostflow.cc: the source C++ code of the minimum-cost flow algorithm.
g++ KnotFold_mincostflow.cc -o KnotFold_mincostflow -std=c++0x -O2 cd example
./run_example.shWe provide training code for KnotFold.
Distributed under the MIT License. See LICENSE for more information.