RNAPKplex - manual page for RNAPKplex 2.6.4
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)
- Command line options for input and output (pre-)processing
- --noconv
- Do not automatically substitute nucleotide "T" with
"U".
- (default=off)
- 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 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.
- 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.
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
If in doubt our program is right, nature is at fault. Comments
should be sent to rna@tbi.univie.ac.at.