Rna2 Dfold

# 1) Compute MFE representatives and partition-function statistics
cat <<'EOF' | RNA2Dfold -p
GGGAAAUCC
(((...)))
((.....))
EOF

# 2) Restrict the explored distance range to both references
cat input.txt | RNA2Dfold -p -K 10 -L 10

# 3) Backtrack samples from one specific neighborhood
cat input.txt | RNA2Dfold -p --stochBT=100 --neighborhood=3:5

Recommended Workflow

1. Prepare input: an RNA sequence plus two reference structures in dot-bracket notation
2. Run RNA2Dfold -p to compute partition function and Gibbs free energy for each k,l neighborhood
3. Use --stochBT=INT to generate Boltzmann samples from specified neighborhoods
4. Analyze MFE representatives and sampled structures across distance classes

Guardrails

• Requires exactly two reference structures in dot-bracket notation as input alongside the sequence
• Distance bounds -K and -L must accommodate the desired neighborhood range
• --stochBT only makes sense together with -p