Rnainverse

# 3) Keep selected nucleotides fixed by using lowercase letters
printf '(((...)))\nNNaaNNNNN\n@\n' | RNAinverse

Recommended Workflow

1. Prepare target structure(s) in bracket notation and optional starting sequence(s)
2. Run RNAinverse with appropriate flags (e.g., -R for repeated search, -Fp for partition function mode)
3. Pipe or type structure and sequence pairs to stdin; use @ or EOF to end input
4. Review output: best sequence found, Hamming distance, and structure distance if unsuccessful

Guardrails

• Input structures must be valid bracket notation; malformed input causes unpredictable behavior
• A starting sequence of "N"s or a blank line randomizes the search; lowercase letters are held fixed
• Unsuccessful searches append a structure distance; verify output matches target structure before use