rnaplex

Quick Start

• Command: RNAplex -q <query.fa> -t <target.fa>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAplex
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Use RNAplex when you want to scan a query RNA against a longer target and rank likely hybridization sites.
• It is most appropriate for probe-like or small-RNA-like searches where only inter-molecular base pairs are modeled.
• Use -a when you already have RNAplfold accessibility profiles and want accessibility-aware target scoring.
• Use -p and -Q when the question is probe melting behavior rather than a generic interaction screen.

Common Patterns

# 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

Recommended Workflow

1. Prepare query and target RNA sequences in FASTA files
2. (Optional) Generate accessibility profiles using RNAplfold if incorporating accessibility effects
3. Run RNAplex -q <query.fa> -t <target.fa> [-a <accessibility_dir>] to compute duplex structures
4. Parse output: each line contains dot-bracket structure (strands separated by "&"), position ranges, and energy in kcal/mol

Guardrails

• Only inter-molecular base pairs are considered; intra-molecular folding is ignored
• Default maximal interaction length is 40 nt; adjust with -l for longer interactions
• Accessibility profiles must be pre-computed with RNAplfold and provided via -a option