Rnasnoop

Common Patterns

# Basic H/ACA snoRNA target search
RNAsnoop -s sno.fa -t target.fa

# Add accessibility profiles from RNAplfold
RNAsnoop -s sno.fa -t target.fa -P plfold_profiles/

# Add accessibility profiles from RNAup
RNAsnoop -s sno.fa -t target.fa -U rnaup_profiles/

# Tighten stem-length and energy filters for stricter candidate selection
RNAsnoop -s sno.fa -t target.fa -h 6 -i 80 -q -1200

Recommended Workflow

1. Prepare query file containing the H/ACA snoRNA sequence and target file containing the RNA sequence to search
2. Run RNAsnoop -s <query.fa> -t <target.fa> to compute hybridization structures
3. Review output: dot-bracket structures with <> for snoRNA intramolecular interactions and () for intermolecular duplexes, including energy values in kcal/mol
4. Optionally provide accessibility profiles via -P (RNAplfold) or -U (RNAup) to improve target prediction accuracy

Guardrails

• This tool is specialized for H/ACA snoRNA target prediction only; for general RNA-RNA interactions use RNAduplex, RNAup, RNAcofold, or RNAplex instead
• Energy threshold options expect values in decacal/mol (not kcal/mol); a threshold of -2.8 kcal/mol should be specified as -280
• Default parameter values assume typical H/ACA snoRNA stem lengths (5-120 nt) and duplex-box distances (11-16 nt); adjust -h/-i and -j/-k if your snoRNA differs significantly
• RNAsnoop -h does not show help; -h is the minimal stem length option, so use --help for usage text