RNAPLEX(1)

🦋 RNAplex · User Commands · Section 1 🦋

✨ NAME ✨

RNAplex - manual page for RNAplex 2.7.0 🌸

📜 SYNOPSIS 📜

RNAplex [options]

💖 DESCRIPTION 💖

RNAplex 2.7.0 🎀

Find targets of a query RNA 🎯

okay bestie, RNAplex reads two RNA sequences from stdin or <filename> and computes the optimal and suboptimal secondary structures for their hybridization 🫶. The calculation is simplified because it only allows inter-molecular base pairs, so no pairing within the same strand 🧚. Accessibility effects can be estimated by RNAplex if you give it a RNAplfold accessibility profile 💅. The optimal and suboptimal structures get written to stdout, one structure per line ✨.

Each line has:

• The structure in dot bracket format, with a & separating the two strands.
• The range of the structure in the two sequences, in the format from,to : from,to.
• The energy of the duplex structure in kcal/mol.

This format is especially iconic for computing the hybrid structure between a small probe sequence and a long target sequence 🔥.

• -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 🗂️
• --version — Print version and exit 🏷️
• -v, --verbose — Be verbose 🗣️ (default=off). This lowers the log level so even INFO messages get passed through.

📥 I/O Options

Command line options for input and output (pre-)processing. This is the stuff that gets your sequences in and out, plus any pre-processing 💌.

• -q, --query=STRING — File containing the query sequence 💅. You can pipe input sequences to RNAplex or hand them over in a query file with -q. Heads up: using -q implies that -t is also used 👀.
• -t, --target=STRING — File containing the target sequence 🎯. You can pipe input sequences to RNAplex or give them in a target file with -t. Heads up: using -t implies that -q is also used 👀.
• -a, --accessibility-dir=STRING — Location of the accessibility profiles 📂. This switches the accessibility modes on and tells RNAplex which directory holds the accessibility profiles generated by RNAplfold.
• -b, --binary — Allow reading and parsing of memory dumped opening energy files 🧠 (default=off). The -b option lets you read and process opening energy files saved in binary format ⚡. This can reduce the time needed to process those files by a factor of 500x-1000x 🚀. RNAplex recognizes the matching opening energy files by looking for files named after the sequence that contain the suffix _openen_bin. If you need more info on making binary opening energy files, check out the RNAplfold man page 📖.
• --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. 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=RNAplex.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

Options that change how RNAplex does its computing 🪄.

• -l, --interaction-length=INT — Maximal length of an interaction (default=40) 📏. This is the maximal allowed length of an interaction.
• -c, --extension-cost=INT — Cost added to each nucleotide in a duplex (default=0) 💸. This is the cost of extending a duplex by one nucleotide, which helps you find compact duplexes with few or small bulges or internal loops 🌸. It's only useful when no accessibility profiles are available. This option is disabled if accessibility profiles are used (-a option) 🙅.
• -p, --probe-mode — Compute Tm for probes 🌡️ (default=off). Use this if you want to compute the melting temperature of your probes.
• -Q, --probe-concentration=DOUBLE — Set the probe concentration for the Tm computation 🧪 (default=0.1).
• -N, --na-concentration=DOUBLE — Set the Na+ concentration for the Tm computation 🧂 (default=1.0).
• -M, --mg-concentration=DOUBLE — Set the Mg2+ concentration for the Tm computation 🧲 (default=1.0).
• -K, --k-concentration=DOUBLE — Set the K+ concentration for the Tm computation 🍌 (default=1.0).
• -U, --tris-concentration=DOUBLE — Set the tris+ concentration for the Tm computation 🧴 (default=1.0).
• -f, --fast-folding=INT — Speedup of the target search 🏎️ (default=0). This option decides whether backtracking happens (-f 0, -f 2) or not (-f 1).
  • -f 0: the structure is computed with the standard energy model. It's the slowest and most precise mode of RNAplex 💎.
  • -f 2: the structure is computed with the approximated plex model. If a lot of targets come back, this can seriously boost RNAplex's runtime ⚡.
  • -f 1: the fastest mode, since no structures get recomputed 🚀.
• -V, --scale-accessibility=DOUBLE — Rescale all opening energy by a factor V 🎚️ (default=1.0). This is the scale factor for the accessibility. If V is set to 1, the scaling has no effect on the accessibility.
• -A, --alignment-mode — Tells RNAplex to compute interactions based on alignments 👯 (default=off). If -A is set, RNAplex expects clustalw files as input for the -q and -t options.
• -k, --convert-to-bin — If set, RNAplex converts all opening energy files in the directory set by the -a option into binary opening energy files 🔄 (default=off). RNAplex can turn existing text formatted opening energy files into binary formatted ones. In this mode, RNAplex does not compute interactions.
• -z, --duplex-distance=INT — Distance between the target 3' ends of two consecutive duplexes 📐 (default=0). This should be set to the maximal length of interaction to get good results. A smaller z leads to larger overlaps between consecutive duplexes 🫠.
• -e, --energy-threshold=DOUBLE — Minimal energy for a duplex to be returned 🎯 (default=-100000). This threshold is set on the total energy of interaction, i.e. the hybridization energy corrected for opening energy if -a is set, or the energy corrected by -c. If unset, only the mfe will be returned 👑.
• -L, --WindowLength=INT — How large the region around the target site should be when redrawing the alignment interaction 🖼️ (default=1). This lets you set how big the surrounding region is when generating the alignment figure of the interaction 💜.

…part 2 picks up with Structure Constraints 🎀

✨ REFERENCES ✨

okay bestie, this section is basically the citations hall of fame 🦋📚 if you use RNAplex for your work, the authors literally want you to cite these papers, so here's the whole lineup:

• 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 calculation of duplex structure is based on a dynamic programming algorithm originally developed by Rehmsmeier and, in parallel, by Hofacker. That's the core math behind the duplex stuff, no cap 🧚

• H. Tafer and I.L. Hofacker (2008), "RNAplex: a fast tool for RNA-RNA interaction search.", Bioinformatics: 24(22), pp 2657-2663 💖 this is the RNAplex paper itself, so it's kind of a must-cite 👑
• S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster (1993), "RNA multi-structure landscapes", Euro Biophys J: 22, pp 13-24 🦋

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 🫶

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✨ AUTHOR ✨

the brains behind this 🧠💅 are Hakim Tafer and Ivo L. Hofacker. iconic duo, literally. 👑

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✨ REPORTING BUGS ✨

okay so the official vibe here is "if in doubt, our program is right, nature is at fault" 💀🙈 lol. but if something's actually broken, send your comments to rna@tbi.univie.ac.at 📬🫶

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RNAplex 2.7.0 released February 2026 and this manual page is for RNAPLEX(1), so that's the whole page, bestie! 🌈✨ stay iconic and keep those RNAs folding 💜🧚