rnainverse

name	rnainverse
description	Use when searching for RNA sequences that fold into a predefined secondary structure, inverting RNA folding predictions to find sequences matching target bracket notation structures.
disable-model-invocation	true
user-invocable	true

rnainverse

Quick Start

• Command: RNAinverse
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAinverse
• Reference: See references/help.md for full option details

When To Use This Tool

• Design sequences that fold into a target dot-bracket structure.
• Explore inverse-folding solutions instead of evaluating one fixed sequence.
• Hold some nucleotides fixed while randomizing the rest.
• Repeat the search many times to obtain alternative candidate sequences.

Common Patterns

# 1) Search from an all-N random starting sequence
printf '(((...)))\nNNNNNNNNN\n@\n' | RNAinverse

# 2) Repeat the inverse-folding search multiple times
printf '(((...)))\nNNNNNNNNN\n@\n' | RNAinverse -R 20

# 3) Keep selected nucleotides fixed by using lowercase letters
printf '(((...)))\nNNaaNNNNN\n@\n' | RNAinverse

Recommended Workflow

1. Prepare target structure(s) in bracket notation and optional starting sequence(s)
2. Run RNAinverse with appropriate flags (e.g., -R for repeated search, -Fp for partition function mode)
3. Pipe or type structure and sequence pairs to stdin; use @ or EOF to end input
4. Review output: best sequence found, Hamming distance, and structure distance if unsuccessful

Guardrails

• Input structures must be valid bracket notation; malformed input causes unpredictable behavior
• A starting sequence of "N"s or a blank line randomizes the search; lowercase letters are held fixed
• Unsuccessful searches append a structure distance; verify output matches target structure before use