Provided by: vienna-rna_2.6.4+dfsg-1build2_amd64 
NAME
RNAPKplex - manual page for RNAPKplex 2.6.4
SYNOPSIS
RNAPKplex [OPTION]...
DESCRIPTION
RNAPKplex 2.6.4
predicts RNA secondary structures including pseudoknots
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 of those two intervals. The
algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space. The algorithm furthermore always considers
dangle=2 model.
It also produces a PostScript file with a plot of the pseudoknot-free secondary structure graph, in
which the bases forming the pseuodknot are marked red.
Sequences are read in a simple text format where each sequence occupies a single line. Each sequence may
be preceded by a line of the form
> name
to assign a name to the sequence. If a name is given in the input, the
PostScript file "name.ps" is produced for the structure graph. Other- wise the file name defaults to
PKplex.ps. Existing files of the same name will be overwritten. The input format is similar to fasta
except that even long sequences may not be interrupted by line breaks, and the header lines
are optional. The program will continue to read new sequences until a line consisting of the single
character @ or an end of file condition is encountered.
-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)
I/O Options:
Command line options for input and output (pre-)processing
--noconv
Do not automatically substitute nucleotide "T" with "U".
(default=off)
Algorithms:
Select additional algorithms which should be included in the calculations.
-c, --cutoff=FLOAT
Report only base pairs with an average probability > cutoff in the dot plot.
(default=`0.01')
-e, --energyCutoff=DOUBLE
Energy cutoff or pseudoknot initiation cost. Minimum energy gain of a pseudoknot interaction for
it to be returned. Pseudoknots with smaller energy gains are rejected.
(default=`-8.10')
-s, --subopts=DOUBLE
print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is
smaller than the given value.
(default=`0.0')
NOTE: The final energy of a structure is calculated as 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 takes the pseudoknot interaction energy into account, so the final
energy differences may be bigger than the specified value (default=0.).
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
--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. --nsp="-GA" will allow GA and AG
pairs. Nonstandard pairs are given 0 stacking energy.
--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
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, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.
RNAPKplex 2.6.4 January 2025 RNAPKPLEX(1)