RNA Design
Overview
In this tutorial, we will walk through how to set up and use the OmniGenomeModelforRNADesign class to design RNA sequences. We will cover the following topics:
- Setting up the model
- Running RNA design
- Saving and loading results
- Fine-tuning the parameters
- Visualizing RNA structures
Setting up the model
Running RNA design
# Define the target RNA structure
structure = "(((....)))" # Example of a simple RNA hairpin structure
# Run the genetic algorithm to design RNA sequences
best_sequences = model.run_rna_design(
structure=structure,
mutation_ratio=0.5,
num_population=100,
num_generation=100
)
# Print the best sequence(s)
print("Best RNA sequences:", best_sequences)
Best RNA sequences: ['GCTGCTGGGC', 'GCTGTGGGGC', 'GCCAGCTGGC', 'GCTCTGGAGC', 'GCTGATGGGC', 'GGTGGCAGCC', 'GCCAAAGGGC', 'GCTGGAGGGC', 'GCCAAAGGGC', 'CGGATTCCCG', 'GCTCTCAAGC', 'GCTGTGGGGC', 'GGGCTTTCCC', 'GCTCAAGGGC', 'GCGCGCGCGC', 'CGCCTCGGCG', 'GCTGAGAGGC', 'GCTGCAGGGC', 'GCTGAAGGGC', 'GGCGAGGGCC', 'GCTAGGAGGC', 'GGGCTTGCCC', 'GGGATGGCCC', 'GCTGCCAAGC', 'GGCGAGGGCC', 'GCTGGCGGGC', 'GCCTTTTGGC', 'GGTGAAGGCC', 'GGCGGCGGCC', 'GCGGCTGCGC', 'GCTGCATGGC', 'GCTGTGGGGC', 'CGCGCGGGCG', 'GGTGCCCGCC', 'TGGAACCCCA', 'GCCCATGGGC', 'CCGAAGCCGG', 'GGGGGGGCCC', 'GCTGCATAGC', 'GCCCTCTGGC', 'GCCGCGGGGC', 'GCTACATGGC', 'GCGGGAGCGC', 'GGTGGCTGCC', 'GCCGTGGGGC', 'GCGCCCCCGC', 'GGTGTCAGCC', 'GGTGTGGGCC', 'GCTCCCGGGC', 'GCTGAGGAGC', 'GCTGCTGGGC', 'GGCCTTCGCC', 'GCGCCCCCGC', 'GCCCTTGGGC', 'GCCGTGGGGC', 'GGCGGCGGCC', 'CGTGCTGACG', 'CCTGAGGAGG', 'GCTACTTGGC', 'TGCGAGGGCA', 'GGCAAAGGCC', 'GCTGAAGAGC', 'CGGCTTGCCG', 'GGGCTTGCCC', 'GCTGAAGAGC', 'GCTGAAGGGC', 'GCCAGTGGGC', 'GGCGCGGGCC', 'GCGGAGGCGC', 'CCTGAGGGGG', 'GCGAAACCGC', 'GCTGAGGGGC', 'GCTTGCAGGC', 'GCTTTCTGGC', 'GGGCTGGCCC', 'GCCATGAGGC', 'GAGGAAGCTC', 'GCTGAAGAGC', 'GCTGCAAGGC', 'CGGGCGGCCG', 'GCCGCGGGGC', 'GCGCGCGCGC', 'CCTGAGGGGG', 'GGGGCTGCCC', 'GCTGAGAGGC', 'GCTAAATGGC', 'GCCGGCAGGC', 'GCCGCTGGGC', 'GCTGGAGGGC', 'GGCGGCGGCC'] In this tutorial, we:
Defined the RNA structure Ran the genetic algorithm for RNA design