Provided by: vienna-rna_2.7.0+dfsg-1_amd64 
NAME
RNA2Dfold - manual page for RNA2Dfold 2.7.0
SYNOPSIS
RNA2Dfold [OPTION]...
DESCRIPTION
RNA2Dfold 2.7.0
Compute MFE structure, partition function and representative sample structures of k,l neighborhoods
The program partitions the secondary structure space into (basepair)distance classes according to two
fixed reference structures. It expects a sequence and two secondary structures in dot-bracket notation as
its inputs. For each distance class, the MFE representative, Boltzmann probabilities and Gibbs free
energy is computed. Additionally, a stochastic backtracking routine allows one to produce samples of
representative suboptimal secondary structures from each partition
-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 such that even INFO messages are passed through.
I/O Options:
Command line options for input and output (pre-)processing
-j, --numThreads=INT
Set the number of threads used for calculations (only available when compiled with OpenMP support)
--noconv
Do not automatically substitute nucleotide "T" with "U".
(default=off)
--log-level=level
Set log level threshold. (default=`2')
By default, any log messages are filtered such that only warnings (level 2) or errors (level 3)
are printed. This setting allows for specifying the log level threshold, where higher values
result in fewer information. Log-level 5 turns off all messages, even errors and other critical
information.
--log-file[=filename]
Print log messages to a file instead of stderr. (default=`RNA2Dfold.log')
--log-time
Include time stamp in log messages.
(default=off)
--log-call
Include file and line of log calling function.
(default=off)
Algorithms:
Select additional algorithms which should be included in the calculations. The Minimum free
energy (MFE) and a structure representative are calculated in any case.
-p, --partfunc
calculate partition function and thus, Boltzmann probabilities and Gibbs free energy
(default=off)
--stochBT=INT
backtrack a certain number of Boltzmann samples from the appropriate k,l neighborhood(s)
--neighborhood=<k>:<l>
backtrack structures from certain k,l-neighborhood only, can be specified multiple times
(<k>:<l>,<m>:<n>,...)
-K, --maxDist1=INT
maximum distance to first reference structure
If this value is set all structures that exhibit a basepair distance greater than maxDist1 will be
thrown into a distance class denoted by K=L=-1
-L, --maxDist2=INT
maximum distance to second reference structure
If this value is set all structures that exhibit a basepair distance greater than maxDist1 will be
thrown into a distance class denoted by K=L=-1
-S, --pfScale=DOUBLE
In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to
avoid overflows).
(default=`1.07')
The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences.
--noBT do not backtrack structures, calculate energy contributions only
(default=off)
-c, --circ
Assume a circular (instead of linear) RNA molecule.
(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 accompany your distribution. See the
RNAlib documentation for details on the file format. The placeholder file name 'DNA' can be used
to load DNA parameters without the need to actually specify any input file.
-4, --noTetra
Do not include 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 additionally using the following parameters
-d, --dangles=INT
How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops
(possible values="0", "2" default=`2')
With -d2 dangling energies will be added for the bases adjacent to a helix on both sides in any
case. The option -d0 ignores dangling ends altogether (mostly for debugging).
--noGU Do not allow GU pairs.
(default=off)
--noClosingGU
Do not allow GU pairs at the end of helices.
(default=off)
--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
R. Lorenz, C. Flamm, I.L. Hofacker (2009), "2D Projections of RNA folding Landscapes", GI, Lecture Notes
in Informatics, German Conference on Bioinformatics 2009: 157, pp 11-20
M. Zuker, P. Stiegler (1981), "Optimal computer folding of large RNA sequences using thermodynamic and
auxiliary information", Nucl Acid Res: 9, pp 133-148
J.S. McCaskill (1990), "The equilibrium partition function and base pair binding probabilities for RNA
secondary structures", Biopolymers: 29, pp 1105-1119
I.L. Hofacker and P.F. Stadler (2006), "Memory Efficient Folding Algorithms for Circular RNA Secondary
Structures", Bioinformatics
D. Adams (1979), "The hitchhiker's guide to the galaxy", Pan Books, London
The calculation of mfe structures is based on dynamic programming algorithm originally developed by M.
Zuker and P. Stiegler. The partition function algorithm is based on work by J.S. McCaskill.
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
Ronny Lorenz
REPORTING BUGS
If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.
RNA2Dfold 2.7.0 September 2025 RNA2DFOLD(1)