RNAPKPLEX(1)

🦋 RNAPKPLEX(1) 🦋

okay bestie, this is the User Commands page for RNAPKPLEX(1), and it is iconic 💅 let's get into it ✨

✨ NAME ✨

RNAPKplex, the manual page for RNAPKplex 2.7.0 🌸

🫶 SYNOPSIS 🫶

RNAPKplex [OPTION]...

that's the whole vibe: run RNAPKplex and toss in as many [OPTION]s as you want 💖

💖 DESCRIPTION 💖

RNAPKplex 2.7.0 is the one that predicts RNA secondary structures, including pseudoknots 🧚

so here's the tea: it computes RNA secondary structures by first making two sequence intervals accessible and unpaired using the algorithm of RNAplfold, and then calculating the energy of the interaction between those two intervals 🦋 the algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space, which is a lot ngl 💀 it also always considers the dangle=2 model, no exceptions 👑

it also spits out a PostScript file with a plot of the pseudoknot-free secondary structure graph, where the bases forming the pseudoknot get marked red 🎀

sequences are read in a simple text format where each sequence takes up a single line 🍓 each sequence can be preceded by a line that looks like this:

> name

and that gives the sequence a name. if you give it a name in the input, the PostScript file "name.ps" gets produced for the structure graph. if you don't, the file name defaults to PKplex.ps 🌈

Heads up bestie: existing files with the same name will be overwritten, so no take-backs 💀

the input format is basically like fasta, EXCEPT even long sequences can't be interrupted by line breaks, and the header lines are optional 🫶 the program keeps reading new sequences until it hits a line consisting of just the single character @, or an end of file condition 💜

🌸 Basic Options 🌸

• -h, --help — Print help and exit 🌸
• --detailed-help — Print help, including all details and hidden options, and exit 🔍
• --full-help — Print help, including hidden options, and exit
• -V, --version — Print version and exit
• -v, --verbose — Be verbose. (default=off) Lower the log level setting so even INFO messages get passed through.

🎀 I/O Options 🎀

Command line options for input and output (pre-)processing 🍓

• --noconv — Don't auto-swap nucleotide "T" for "U". Do not automatically substitute nucleotide "T" with "U". (default=off)
• --log-level=level — Set the log level threshold. (default=`2') By default, log messages are filtered so only warnings (level 2) or errors (level 3) get printed. This setting lets you pick the threshold, where higher values mean fewer messages. Log-level 5 turns off all messages, even errors and other critical info 🙈
• --log-file[=filename] — Print log messages to a file instead of stderr. (default=`RNAPKplex.log')
• --log-time — Include a time stamp in log messages. (default=off)
• --log-call — Include the file and line of the log calling function. (default=off)

🔥 Algorithms 🔥

Select additional algorithms to include in the calculations 💅

• -c, --cutoff=FLOAT — Only consider unpaired probabilities > cutoff for putative PK sites. (default=`1e-6')
• -e, --energyCutoff=DOUBLE — The energy cutoff, aka the pseudoknot initiation cost. This is the minimum energy gain a pseudoknot interaction needs to be returned. Pseudoknots with smaller energy gains get rejected. (default=`-8.10')
• -s, --subopts=DOUBLE — Print suboptimal structures whose energy difference from the optimum pseudoknot is smaller than the given value. (default=`0.0') NOTE: the final energy of a structure is the sum of the pseudoknot interaction energy, the penalty for initiating a pseudoknot, and the energy of the pseudoknot-free part of the structure. The -s option only counts the pseudoknot interaction energy, so the final energy differences may be bigger than the value you set (default=0.) 🧐
• --betaScale=DOUBLE — Set the scaling of the Boltzmann factors. (default=`1.') this argument scales the thermodynamic temperature in the Boltzmann factors independently from the temperature of the individual loop energy contributions. So the Boltzmann factors become 'exp(- dG/(kT*betaScale))', where 'k' is the Boltzmann constant, 'dG' is the free energy contribution of the state, and 'T' is the absolute temperature 🌡️
• -S, --pfScale=DOUBLE — When calculating the pf, use scale*mfe as an estimate for the ensemble free energy (this is used to avoid overflows). (default=`1.07') The default is 1.07, and useful values are 1.0 to 1.2. Occasionally needed for long sequences 🦋

🌈 Energy Parameters 🌈

Energy parameter sets can be adapted or loaded from user-provided input files ✨

• -T, --temp=DOUBLE — Rescale energy parameters to a temperature of temp C. The default is 37C. (default=`37.0')
• -P, --paramFile=paramfile — Read energy parameters from paramfile instead of the default parameter set. Different sets of energy parameters for RNA and DNA should accompany your distribution. See the RNAlib documentation for the file format details. The placeholder file name 'DNA' can be used to load DNA parameters without needing to actually specify any input file 🧬
• -4, --noTetra — Don't include the special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. (default=off) Mostly for testing.
• --salt=DOUBLE — Set the salt concentration in molar (M). Default is 1.021M.

🧚 Model Details 🧚

Tweak the energy model and pairing rules even more with these parameters 💜

• --noLP — Produce structures without lonely pairs (helices of length 1). (default=off) For partition function folding, this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.
• --noGU — Do not allow GU pairs. (default=off)
• --noClosingGU — Do not allow GU pairs at the end of helices. (default=off)
• --nsp=STRING — Allow other pairs in addition to the usual AU, GC, and GU pairs. The argument is a comma-separated list of extra allowed pairs. If the first character is a "-", then AB implies that both AB and BA are allowed pairs; e.g. --nsp="-GA" will allow GA and AG pairs. Nonstandard pairs get 0 stacking energy 🌸
• --helical-rise=FLOAT — Set the helical rise of the helix in Angstrom units. (default=`2.8') Use with caution! This value will be re-set automatically to 3.4 if DNA parameters are loaded via -P DNA and no further value is provided ⚠️
• --backbone-length=FLOAT — Set the average backbone length for looped regions in Angstrom units. (default=`6.0') Use with caution! This value will be re-set automatically to 6.76 if DNA parameters are loaded via -P DNA and no further value is provided ⚠️

📚 REFERENCES 📚

if you use this program in your work, you might want to cite:

• R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26 🧠
• I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125, pp 167-188 📖
• R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13 ✨

the energy parameters are taken from:

• D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292 💜
• D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282 🩷

🎀 AUTHOR 🎀

Wolfgang Beyer 👑

🐛 REPORTING BUGS 🐛

if in doubt, our program is right and nature is at fault 💅 send comments to rna@tbi.univie.ac.at.

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that's the whole tea, bestie! RNAPKplex 2.7.0, February 2026 🫶🦋✨