Provided by: vienna-rna_2.6.4+dfsg-1build1_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.