Random Sequence (Pknot?) generator script

Gameplay and Strategies
1

This python script is designed to give you a randomly generated 127 nucleotide segment with a unique barcode. The script is currently set to generate 100 sequences but you can change it to generate as many sequences as you would like.

As I have tested it I have found 2 things so far
1.) The 2nd hairpin doesn’t always form on it’s own
2.) Eternafold only predicts pseudoknots in approximately 50% of the sequences that are generated.

There may be other things wrong with it I am very new to programming feel free to edit or change anything as needed. Preformatted text

Here is the script:

import random
import string

def generate_rna_sequence(length):
    return ''.join(random.choice('ACGU') for _ in range(length))

def generate_barcode():
    barcode = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(10))
    return barcode

def generate_pseudoknot_rna_sequences(num_sequences, sequence_length):
    rna_sequences = set()
    while len(rna_sequences) < num_sequences:
        sequence = generate_rna_sequence(sequence_length)
        barcode = generate_barcode()
        rna_sequences.add(sequence + barcode + sequence[::-1])
    return list(rna_sequences)

num_sequences = 100
sequence_length = 129

rna_sequences = generate_pseudoknot_rna_sequences(num_sequences, sequence_length)

# Printing the generated sequences
for i, sequence in enumerate(rna_sequences):
    print(f"Sequence {i + 1}: {sequence}")
2

I’m not sure what you were trying to do with an alphanumeric barcode. If you take the random sequence generator and run it to generate 100 x 100nt sequences you can paste those into the Pseudoknot Finder booster though. I found 47 in one run.

#!/usr/bin/env python3
import random
import string

def generate_rna_sequence(length):
    return ''.join(random.choice('ACGU') for _ in range(length))

def generate_pseudoknot_rna_sequences(num_sequences, sequence_length):
    rna_sequences = set()
    while len(rna_sequences) < num_sequences:
        sequence = generate_rna_sequence(sequence_length)
        rna_sequences.add(sequence)
    return list(rna_sequences)

num_sequences = 100
sequence_length = 100

rna_sequences = generate_pseudoknot_rna_sequences(num_sequences, sequence_length)

# Printing the generated sequences
for i, sequence in enumerate(rna_sequences):
    print(f"{sequence}")
1 Like
3

Well, you need to replace your code with below code.

import random
import string

def generate_rna_sequence(length):
    return ''.join(random.choice('ACGU') for _ in range(length))

def generate_barcode():
    barcode = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(10))
    return barcode

def generate_pseudoknot_rna_sequences(num_sequences, sequence_length):
    rna_sequences = set()
    while len(rna_sequences) < num_sequences:
        sequence = generate_rna_sequence(sequence_length)
        barcode = generate_barcode()
        rna_sequences.add(sequence + barcode + sequence[::-1])
    return list(rna_sequences)

num_sequences = 100
sequence_length = 129

rna_sequences = generate_pseudoknot_rna_sequences(num_sequences, sequence_length)

# Printing the generated sequences
for i, sequence in enumerate(rna_sequences):
    print(f"Sequence {i + 1}: {sequence}")

Thanks