Use when screening a small query RNA against longer target RNA sequences for inter-molecular hybridization sites, especially when optional RNAplfold accessibility profiles should influence the ranking.
RNAplex -q <query.fa> -t <target.fa>/home/vimalinx/miniforge3/envs/bio/bin/RNAplexreferences/help.md for complete options and detailsRNAplex when you want to scan a query RNA against a longer target and rank likely hybridization sites.-a when you already have RNAplfold accessibility profiles and want accessibility-aware target scoring.-p and -Q when the question is probe melting behavior rather than a generic interaction screen.# Basic query-vs-target interaction search
RNAplex -q query.fa -t target.fa
# Include precomputed accessibility profiles from RNAplfold
RNAplex -q query.fa -t target.fa -a plfold_profiles/
# Require stronger interactions and allow longer duplexes
RNAplex -q query.fa -t target.fa -l 60 -e -12
# Probe mode with explicit probe concentration
RNAplex -q query.fa -t target.fa -p -Q 0.5
RNAplex -q <query.fa> -t <target.fa> [-a <accessibility_dir>] to compute duplex structures-l for longer interactions-a option