rnasubopt

name	rnasubopt
description	Use when computing suboptimal RNA secondary structures within an energy range above the minimum free energy, or when sampling structures from the Boltzmann ensemble.
disable-model-invocation	true
user-invocable	true

rnasubopt

Quick Start

• Command: RNAsubopt
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAsubopt
• Full reference: See references/help.md for complete options and parameter details

When To Use This Tool

• Use RNAsubopt when you need a set of plausible secondary structures instead of a single best fold.
• Use -e to enumerate all structures within an energy band above the MFE for short or moderate-length RNAs.
• Use -p when exhaustive enumeration would explode and you instead want Boltzmann-weighted sampling from the ensemble.
• Reach for -z, -D, -c, or -g when the question is specifically about Zuker suboptimals, density of states, circular RNAs, or G-quadruplex-aware folding.
• It is also appropriate when experimental probing data should bias the structure ensemble through --shape or --sp-data.

Common Patterns

# Enumerate structures within 2 kcal/mol of the MFE
printf 'GGGAAAUCC\n' | RNAsubopt -e 2

# Sample 100 structures from the Boltzmann ensemble
printf 'GGGAAAUCC\n' | RNAsubopt -p 100

# Sort enumerated suboptimal structures
printf 'GGGAAAUCC\n' | RNAsubopt -e 2 -s

# Compute density of states instead of explicit structures
printf 'GGGAAAUCC\n' | RNAsubopt -D

Recommended Workflow

1. Prepare RNA sequence input via stdin or specify an input file with -i
2. Select algorithm mode: energy range enumeration (-e), stochastic sampling (-p), or Zuker suboptimals (-z)
3. Run RNAsubopt with appropriate parameters (e.g., -e 3.0 for structures within 3 kcal/mol of MFE, -p 1000 for 1000 sampled structures)
4. Review output containing dot-bracket secondary structures followed by energy values in kcal/mol

Guardrails

• Output size grows exponentially with sequence length and energy range; use conservative -e values or switch to sampling (-p) for long sequences
• Default temperature is 37°C; adjust with -T for non-physiological or organism-specific conditions
• Nucleotide "T" is automatically converted to "U" by default; use --noconv to preserve input exactly