DavidHurst / IRfold

RNA secondary structure prediction through Constraint Programming

I verify that I am the sole author of the programmes contained in this archive, except where explicitly stated to the contrary. David Hurst, 12/08/2023

Table of Contents

/data: Results of experiments and stored dataset (dataset omitted for sake of file size)

/experiment_scripts/experiment_1_: Scripts which run and analyse experiment to show the additive free energy vs union free energy /experiment_scripts/experiment_2_: Scripts which run and analyse experiment to show that validating IR pairs also vaidates IR triplets and quadruplets /experiment_scripts/experiment_3_: Scripts which run and analyse experiment to show the error in the free energy additivity assumption /experiment_scripts/experiment_4_: Scripts which run and analyse experiment to show the performance of the solver for different IRFold variants on a test set of random sequences. /experiment_scripts/experiment_5_*: Scripts which run and analyse experiment to benchmark the performance of IRFold against other models on the bpRNA-1m dataset

/irfold/irfold_base.py: Class defining the IRFoldBase model /irfold/irfold_val1.py: Class defining the IRFoldVal1 model /irfold/irfold_val2.py: Class defining the IRFoldVal2 model /irfold/irfold_corx.py: Class defining the IRFoldCorX model /irfold/irfold_cor2.py: Class used for development and testing of IRFoldCorX /irfold/irfold_cor3.py: Class used for development and testing of IRFoldCorX /irfold/IUPACpal: Binary exe of IUPACpal, used to find IRs

/test: Unit tests for package

IRFold

RNA Secondary Structure Prediction by optimising configurations of found inverted repeats via Constraint Programming. IRFold will only run on Linux due to RNAlib's Python package.

Minimal Install

Assumes Conda installed

1. Clone repository

   git clone https://github.com/DavidHurst/IRFold 
   

2. Move to repository directory

   cd IRFold/
   

3. Create new environment from requirements file

   conda env create -f requirements.yml
   

4. Activate environment

   conda activate irfold
   

5. Run demo script

   python demo.py
   

Install for Experiments

1. Run minimal installation steps above
2. Compile and install ViennaRNA version 2.5.1 to /experiment_scripts/ViennaRNA-2.5.1 from https://www.tbi.univie.ac.at/RNA/
3. Compile and install GLPK version 5.0 to /experiment_scripts/ from https://www.gnu.org/software/glpk/
4. Compile and install IPknot to /experiment_scripts/ipknot from https://github.com/satoken/ipknot
5. Set location of thermodynamic parameters for RNAstructure:

   export DATAPATH=experiment_scripts/RNAstructure/data_tables/
   

6. Run experiment scripts of choice e.g.

   python experiment_scripts/experiment_1_investigate_ir_pair_fe_additivity.py