RNAPALN(1)

📦
version 2.7.0 · 5 versions
, in ubuntu resolute, ubuntu stonking

okay bestie, welcome to the RNApaln manual 🦋 this is the whole tea on how it works, so let's get into it 💅

✨ NAME ✨

RNApaln - manual page for RNApaln 2.7.0 🌸

🎀 SYNOPSIS 🎀

RNApaln [OPTION]...

💖 DESCRIPTION 💖

okay so RNApaln 2.7.0 is an RNA alignment tool that runs on sequence base pairing propensities 🧬 it's giving main character energy ngl

It uses string-alignment techniques to do fast pairwise structural alignments of RNAs. Like RNApdist, it sneaks in secondary structure in an approximate way: it works out base pair probabilities, then boils them down to a vector holding the probability that a base is paired upstream, downstream, or stays unpaired. These pair propensity vectors can then be compared with standard alignment algorithms. Unlike RNApdist, RNApaln does similarity (not distance) alignments, looks at both sequence and structure, and uses affine (rather than linear) gap costs ✨ RNApaln can do semi-local alignments using free end gaps, and a true local alignment mode is planned 👀

The same approach has since been used in the StraL program from Gerhard Steeger's group. Since StraL has optimized parameters and a multiple alignment mode, it'd be the better option right now 🫶

  • -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) It lowers the log level so even INFO messages get passed through 📣

📥 I/O Options 📤

these are the command line options for input and output (pre-)processing 🎀

  • -B, --printAlignment[=filename] — print an "alignment" with gaps of the profiles. The aligned structures get written to filename if you specify it. Otherwise the output goes to stdout, unless the -Xm option is set, in which case "backtrack.file" is used. (default=`stdout')

The following symbols are used:

  • ( / ) — essentially upstream (downstream) paired bases
  • { / } — weakly upstream (downstream) paired bases
  • | — strongly paired bases without preference
  • , — weakly paired bases without preference
  • . — essentially unpaired bases
  • --noconv — do not automatically substitute the nucleotide T with U 🙅‍♀️ (default=off)
  • --log-level=level — set the log level threshold. (default=`2') By default, only warnings (level 2) or errors (level 3) get printed. This lets you pick the threshold, and 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=`RNApaln.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 that should be included in the calculations 💜

  • -X, --mode=pmfc — set the alignment mode to be used. The mode is passed as a single character value. These are the options:
    • 'p' — compare the structures pairwise, that is first with 2nd, third with 4th, etc. This is the default ✨
    • 'm' — calculate the distance matrix between all structures. The output is formatted as a lower triangle matrix 📐
    • 'f' — compare each structure to the first one
    • 'c' — compare continuously, that is i-th with (i+1)th structure
  • --gapo=open — set the gap open penalty
  • --gape=ext — set the gap extension penalty
  • --seqw=w — set the weight of sequence (compared to structure) in the scoring function
  • --endgaps — use free end-gaps (default=off)

🔥 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. Default is 37C. (default=`37.0')
  • -P, --paramFile=paramfile — read energy parameters from paramfile, instead of using the default parameter set. Different sets of energy parameters for RNA and DNA should come with your distribution. See the RNAlib documentation for details on the file format. Passing the placeholder file name "DNA" loads DNA parameters without needing to actually specify any input file 🧬
  • -4, --noTetra — do not include the special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. (default=off) Mostly for testing 🧪
  • --salt=DOUBLE — set salt concentration in molar (M). Default is 1.021M 🧂

🧬 Model Details 🧬

tweak the energy model and pairing rules even more using the following parameters 💅

  • -d, --dangles=INT — how to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops. (default=`2')
    • -d1 — only unpaired bases can participate in at most one dangling end
    • -d2 — this check is ignored, and dangling energies get added for the bases adjacent to a helix on both sides in any case. This is the default for mfe and partition function folding (-p) 👑
    • -d0 — ignores dangling ends altogether (mostly for debugging)
    • -d3 — mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two enclosed pairs in a loop of degree 3, and it works only for mfe folding

Note that with -d1 and -d3 only the MFE computations use this setting, while partition function uses the -d2 setting, i.e. dangling ends get treated differently 🥺

  • --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. Its argument is a comma separated list of additionally allowed pairs. If the first character is a -, then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy 🍓
  • --energyModel=INT — set the energy model. This is a rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (--energyModel 1) or AU (--energyModel 2) pairs
  • --helical-rise=FLOAT — set the helical rise of the helix in units of Angstrom. (default=`2.8')
Use with caution! This value will be re-set automatically to 3.4 in case 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 units of Angstrom. (default=`6.0')
Use with caution! This value will be re-set automatically to 6.76 in case 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
  • Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P (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

👑 AUTHOR 👑

Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer 🫶

🐛 REPORTING BUGS 🐛

If in doubt our program is right, nature is at fault. 🙃 Comments should be sent to rna@tbi.univie.ac.at.

okay bestie that's the whole page 😭💖 it's RNApaln 2.7.0, dated February 2026, filed under RNAPALN(1) 🦋✨ go be iconic 💅

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