rnalfold

name	rnalfold
description	Use when computing locally stable RNA secondary structures with a maximal base pair span, scanning large genomes for short RNA structures, or predicting local RNA folding with Z-score filtering.
disable-model-invocation	true
user-invocable	true

rnalfold

Quick Start

• Command: RNALfold
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNALfold
• Full reference: references/help.md

When To Use This Tool

• Search one long RNA for locally stable structural elements.
• Limit folding to a maximum base-pair span instead of computing one global fold.
• Filter local hits by Z-score when you need stronger statistical support.
• Generate compact local-structure calls for genome-scale scans.

Common Patterns

# 1) Scan a sequence from stdin with default span
echo 'GGGAAAUCCGGGAAAUCC' | RNALfold

# 2) Restrict the maximal base-pair span
echo 'GGGAAAUCCGGGAAAUCC' | RNALfold -L 100

# 3) Report only strongly supported local structures
echo 'GGGAAAUCCGGGAAAUCC' | RNALfold -L 120 -z -2.5

Recommended Workflow

1. Prepare input RNA sequence file or pipe sequence via stdin
2. Run RNALfold with appropriate -L span value for your use case
3. Optionally apply -z for Z-score filtering or --shape for SHAPE-guided prediction
4. Review output listing local structures, energies, and starting positions

Guardrails

• Verify input sequences are valid RNA/DNA (T is auto-converted to U unless --noconv is set)
• The -L span parameter directly affects memory and CPU usage; larger values increase resource demands
• Output may contain overlapping or subsumed structures; use Z-score options to filter results