Use when computing local RNA secondary structure pair probabilities, scanning large genomes for short stable RNA structures, or analyzing unpaired region probabilities across sliding windows.
RNAplfold [OPTION].../home/vimalinx/miniforge3/envs/bio/bin/RNAplfoldreferences/help.md for full option detailsRNAplfold when you care about local secondary structure rather than a single global fold.-u when the downstream question is accessibility or unpaired-region probability for short motifs.# Default local folding over stdin sequence(s)
printf '>seq\nGGGAAAUCC\n' | RNAplfold
# Tune window size and maximal base-pair span for compact local structures
printf '>seq\nGGGAAAUCC\n' | RNAplfold -W 120 -L 80
# Report unpaired probabilities for regions up to length 10
printf '>seq\nGGGAAAUCC\n' | RNAplfold -u 10
# Reduce output noise to stronger local pair probabilities only
printf '>seq\nGGGAAAUCC\n' | RNAplfold -c 0.05
--noconv is set).-W, default 70) and maximum span (-L) based on target structure size.RNAplfold with optional -u for unpaired region probabilities up to specified length.-L (span) explicitly; it limits the maximal separation of base pairs and affects memory/CPU usage.-c cutoff to filter reported base pairs by minimum average probability (default 0.01).-o (--print_onthefly) to save memory by outputting during computation.