rna2-dfold

name	rna2-dfold
description	Use when computing MFE structures, partition functions, and Boltzmann-sampled secondary structures within k,l distance neighborhoods relative to two reference structures for an RNA sequence.
disable-model-invocation	true
user-invocable	true

rna2-dfold

Quick Start

• Command: RNA2Dfold [OPTIONS] < sequence_with_two_structures
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNA2Dfold
• Full reference: See references/help.md for complete options and model details

When To Use This Tool

• Partition RNA secondary structure space by base-pair distance to two reference structures.
• Compare alternative folding neighborhoods around two candidate conformations for the same RNA.
• Compute MFE representatives and, with -p, ensemble statistics for each (k,l) distance class.
• Sample structures from specific neighborhoods with stochastic backtracking.

Common Patterns

# 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