rnados

Quick Start

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

When To Use This Tool

• Use RNAdos when you want a compact view of the folding landscape as counts per energy band instead of explicit suboptimal structures.
• It is useful for judging how broad or narrow the accessible energy landscape is around the MFE.
• Use -e when the default 0 kcal/mol ceiling truncates energy bands you care about.
• Use -j when the build supports OpenMP and the calculation is large enough to benefit from more threads.

Common Patterns

# Density of states for a single RNA sequence
RNAdos -s GGGAAAUCC

# Count structures up to a higher energy threshold
RNAdos -s GGGAAAUCC -e 5

# Run with multiple threads when available
RNAdos -s GGGAAAUCC -j 4

# Recompute the landscape under a different temperature
RNAdos -s GGGAAAUCC -T 25

Recommended Workflow

1. Prepare your RNA sequence in ACGU format
2. Run RNAdos -s SEQUENCE with optional parameters like -T for temperature or --salt for salt concentration
3. Adjust --max-energy threshold if you need to count structures beyond the default 0 kcal/mol
4. Interpret the density of states output to understand the energy distribution of possible structures

Guardrails

• Input sequence must contain only valid RNA nucleotides (A, C, G, U)
• Default max-energy threshold is 0 kcal/mol; increase with -e if higher energy states are relevant
• Temperature defaults to 37°C; specify -T if working under different conditions