rnaheat

name	rnaheat
description	Use when computing RNA specific heat profiles from sequence data to analyze melting behavior and thermal stability across temperature ranges.
disable-model-invocation	true
user-invocable	true

rnaheat

Quick Start

• Command: RNAheat [OPTIONS] [<input>]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAheat
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Compute specific heat curves to study RNA melting behavior.
• Compare thermal stability across sequences or parameter settings.
• Scan a temperature range before choosing a biologically relevant folding temperature.
• Include circular-RNA or G-quadruplex assumptions in thermal profiles.

Common Patterns

# 1) Compute a default heat-capacity profile
echo 'GGGAAAUCC' | RNAheat > heat.tsv

# 2) Restrict the temperature range and step size
echo 'GGGAAAUCC' | RNAheat --Tmin 10 --Tmax 80 --stepsize 0.5 > heat.tsv

# 3) Model a circular RNA with G-quadruplex support
echo 'GGGAAAUCC' | RNAheat --circ --gquad > heat.tsv

Recommended Workflow

1. Prepare input RNA sequence(s) in plain text or FASTA-like format
2. Set temperature range with --Tmin and --Tmax (default 0–100°C) and adjust --stepsize as needed
3. Run RNAheat with appropriate options (e.g., --circ for circular RNA, --gquad for G-quadruplex)
4. Parse output pairs of temperature (°C) and specific heat (kcal/(mol*K)) for downstream analysis

Guardrails

• Output is tabular (temperature, specific heat) to stdout; redirect to file for persistence
• Input stops at a line containing only @ or EOF; ensure proper sequence delimiting
• Smoothing via -m/--ipoints affects curve shape; higher values produce smoother results at cost of resolution