Use when searching an RNA sequence for pseudoknot-forming interactions by combining local accessibility with interaction energy, especially when ordinary pseudoknot-free folding is insufficient.
RNAPKplex [OPTIONS] < input.fasta/home/vimalinx/miniforge3/envs/bio/bin/RNAPKplexreferences/help.md for complete options and detailsRNAPKplex when pseudoknots are central to the structural hypothesis and pseudoknot-free RNA folding tools are not sufficient.-c to suppress weakly accessible candidate sites and -e to demand stronger pseudoknot stabilization.-s when you want near-optimal pseudoknot alternatives instead of only the best one.# Basic pseudoknot search from stdin
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex
# Require stronger energy gain before reporting pseudoknots
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex -e -10
# Filter low-accessibility candidate regions
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex -c 1e-4
# Include near-optimal suboptimal pseudoknot solutions
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex -s 2
RNAPKplex with default parameters to identify potential pseudoknots-e (energy cutoff) or -c (probability cutoff) to filter results as needed-s to explore suboptimal structures within a specified energy rangernapkplex, but the actual executable is capitalized as RNAPKplex