rnapaln

name	rnapaln
description	Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.
disable-model-invocation	true
user-invocable	true

rnapaln

Quick Start

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

When To Use This Tool

• Align two RNAs using both sequence identity and structural propensity.
• Compare related RNAs when plain sequence alignment misses conserved structure.
• Tune gap penalties and sequence-vs-structure weighting explicitly.
• Use semi-local alignment with free end gaps rather than strict end-to-end matching.

Common Patterns

# 1) Align two RNAs from stdin
printf 'AUGCUA\nAUGUUA\n' | RNApaln

# 2) Print the alignment with gaps
printf 'AUGCUA\nAUGUUA\n' | RNApaln -B

# 3) Use free end-gaps and custom gap penalties
printf 'AUGCUA\nAUGUUA\n' | RNApaln --endgaps --gapo=8 --gape=1 --seqw=0.5

Recommended Workflow

1. Prepare input RNA sequences for pairwise comparison
2. Run RNApaln with gap penalties (--gapo, --gape) and sequence weight (--seqw) as needed
3. Use -B to output the alignment with gaps; add --endgaps for semi-local alignment
4. Review alignment output; adjust energy parameters (-T, --salt, -P) for non-standard conditions

Guardrails

• True local alignment mode is not implemented; only semi-local (free end gaps) is supported
• Performs pairwise alignments only; for multiple alignment consider StraL
• Nucleotide T is automatically converted to U unless --noconv is specified