rnaplfold

name	rnaplfold
description	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.
disable-model-invocation	true
user-invocable	true

rnaplfold

Quick Start

• Command: RNAplfold [OPTION]...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAplfold
• Reference: See references/help.md for full option details

When To Use This Tool

• Use RNAplfold when you care about local secondary structure rather than a single global fold.
• It is a good fit for scanning long transcripts or genomic windows for short stable stem-loop regions with bounded base-pair span.
• Use it when you need averaged base-pair probabilities over a sliding window, not just one minimum-free-energy structure.
• Turn on -u when the downstream question is accessibility or unpaired-region probability for short motifs.

Common Patterns

# 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

Recommended Workflow

1. Prepare input sequences in FASTA format (T is auto-converted to U unless --noconv is set).
2. Set window size (-W, default 70) and maximum span (-L) based on target structure size.
3. Run RNAplfold with optional -u for unpaired region probabilities up to specified length.
4. Review output dot plot files for pair probabilities and unpaired probability data.

Guardrails

• Set -L (span) explicitly; it limits the maximal separation of base pairs and affects memory/CPU usage.
• Use -c cutoff to filter reported base pairs by minimum average probability (default 0.01).
• For very large sequences, enable -o (--print_onthefly) to save memory by outputting during computation.