Z-Score Calculator for RNA/DNA MFE Structures

A Python tool that calculates Z-scores for minimum free energy (MFE) structures of RNA/DNA sequences using doublet-preserving shuffling.

Required Libraries

• Biopython (Bio.SeqIO)
• ViennaRNA (RNA)
• NumPy
• SciPy
• Matplotlib
• Seaborn

Usage

python zscore_calculator.py [options] [Fasta 1] [Fasta 2] ...

Arguments

• Positional: One or more FASTA files containing sequences
• -s, --samples: Number of shuffled sequences for background distribution (default: 1000)
• -p, --plotting: Generate energy distribution plots (default: True)
• -o, --output: Output directory path (default: current directory)

Output

• TSV file with Z-scores and p-values
• Energy distribution histograms (PNG files)
• Console output with sequence details and statistics