Use when searching target RNAs for interactions with a query H/ACA snoRNA, especially when the search should respect H/ACA-specific structural constraints and optionally use accessibility profiles.
RNAsnoop -s <query_file> -t <target_file>/home/vimalinx/miniforge3/envs/bio/bin/RNAsnoopRNAsnoop when the biological question is specifically about H/ACA snoRNA target prediction, not general RNA-RNA duplexing.-P or -U when accessibility profiles from RNAplfold or RNAup should be incorporated into target ranking.# 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
RNAsnoop -s <query.fa> -t <target.fa> to compute hybridization structures<> for snoRNA intramolecular interactions and () for intermolecular duplexes, including energy values in kcal/mol-P (RNAplfold) or -U (RNAup) to improve target prediction accuracy-h/-i and -j/-k if your snoRNA differs significantlyRNAsnoop -h does not show help; -h is the minimal stem length option, so use --help for usage text