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.
RNA2Dfold [OPTIONS] < sequence_with_two_structures/home/vimalinx/miniforge3/envs/bio/bin/RNA2Dfoldreferences/help.md for complete options and model details-p, ensemble statistics for each (k,l) distance class.# 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
RNA2Dfold -p to compute partition function and Gibbs free energy for each k,l neighborhood--stochBT=INT to generate Boltzmann samples from specified neighborhoods-K and -L must accommodate the desired neighborhood range--stochBT only makes sense together with -p