--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNASUBOPT "1" "July 2013" "RNAsubopt 2.1.2" "User Commands"
+.SH NAME
+RNAsubopt \- manual page for RNAsubopt 2.1.2
+.SH SYNOPSIS
+.B RNAsubopt
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAsubopt 2.1.2
+.PP
+calculate suboptimal secondary structures of RNAs
+.PP
+reads RNA sequences from stdin and (in the default \fB\-e\fR mode) calculates all
+suboptimal secondary structures within a user defined energy range above the
+minimum free energy (mfe). It prints the suboptimal structures in dot\-bracket
+notation followed by the energy in kcal/mol to stdout. Be careful, the number
+of structures returned grows exponentially with both sequence length and energy
+range.
+.PP
+Alternatively, when used with the \fB\-p\fR option, RNAsubopt produces Boltzmann
+weighted samples of secondary structures.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Print help and exit
+.TP
+\fB\-\-detailed\-help\fR
+Print help, including all details and hidden
+options, and exit
+.TP
+\fB\-\-full\-help\fR
+Print help, including hidden options, and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Print version and exit
+.SS "General Options:"
+.IP
+Below are command line options which alter the general behavior of this
+program
+.TP
+\fB\-C\fR, \fB\-\-constraint\fR
+Calculate structures subject to constraints.
+(default=off)
+.IP
+The program reads first the sequence, then a string containing constraints on
+the structure encoded with the symbols:
+.IP
+\&. (no constraint for this base)
+.IP
+| (the corresponding base has to be paired
+.IP
+x (the base is unpaired)
+.IP
+< (base i is paired with a base j>i)
+.IP
+\f(CW> (base i is paired with a base j<i)\fR
+.IP
+and matching brackets ( ) (base i pairs base j)
+.IP
+With the exception of "|", constraints will disallow all pairs conflicting
+with the constraint. This is usually sufficient to enforce the constraint,
+but occasionally a base may stay unpaired in spite of constraints. PF folding
+ignores constraints of type "|".
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide
+"T" with "U"
+.IP
+(default=off)
+.SS "Algorithms:"
+.IP
+Select the algorithms which should be applied to the given RNA sequence.
+.TP
+\fB\-e\fR, \fB\-\-deltaEnergy\fR=\fIrange\fR
+Compute suboptimal structures with energy in a
+certain range of the optimum (kcal/mol).
+Default is calculation of mfe structure only.
+.TP
+\fB\-\-deltaEnergyPost\fR=\fIrange\fR
+Only print structures with energy within range
+of the mfe after post reevaluation of
+energies.
+.IP
+Useful in conjunction with \fB\-logML\fR, \fB\-d1\fR or \fB\-d3\fR: while the \fB\-e\fR option specifies
+the range before energies are re\-evaluated, this option specifies the maximum
+energy after re\-evaluation.
+.TP
+\fB\-s\fR, \fB\-\-sorted\fR
+Sort the suboptimal structures by energy.
+(default=off)
+.IP
+Since the sort in is done in memory, this becomes impractical when the number
+of structures produced goes into millions. In such cases better pipe the
+output through "sort +1n".
+.TP
+\fB\-p\fR, \fB\-\-stochBT\fR=\fInumber\fR
+Instead of producing all suboptimals in an
+energy range, produce a random sample of
+suboptimal structures, drawn with
+probabilities equal to their Boltzmann
+weights via stochastic backtracking in the
+partition function. The \fB\-e\fR and \fB\-p\fR options are
+mutually exclusive.
+.TP
+\fB\-S\fR, \fB\-\-pfScale\fR=\fIscaling\fR factor
+In the calculation of the pf use scale*mfe as
+an estimate for the ensemble free energy
+(used to avoid overflows). Needed by
+stochastic backtracking
+.IP
+The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for
+long sequences.
+You can also recompile the program to use double precision (see the README
+file).
+.TP
+\fB\-c\fR, \fB\-\-circ\fR
+Assume a circular (instead of linear) RNA
+molecule.
+.IP
+(default=off)
+.TP
+\fB\-D\fR, \fB\-\-dos\fR
+Compute density of states instead of secondary
+structures
+.IP
+(default=off)
+.IP
+This option enables the evaluation of the number of secondary structures in
+certain energy bands arround the MFE.
+.TP
+\fB\-z\fR, \fB\-\-zuker\fR
+Compute Zuker suboptimals instead of all
+suboptimal structures within an engery band
+arround the MFE.
+.IP
+(default=off)
+.SS "Model Details:"
+.TP
+\fB\-T\fR, \fB\-\-temp\fR=\fIDOUBLE\fR
+Rescale energy parameters to a temperature of
+temp C. Default is 37C.
+.TP
+\fB\-4\fR, \fB\-\-noTetra\fR
+Do not include special tabulated stabilizing
+energies for tri\-, tetra\- and hexaloop
+hairpins. Mostly for testing.
+.IP
+(default=off)
+.TP
+\fB\-d\fR, \fB\-\-dangles\fR=\fIINT\fR
+How to treat "dangling end" energies for
+bases adjacent to helices in free ends and
+multi\-loops
+.IP
+(default=`2')
+.IP
+With \fB\-d1\fR only unpaired bases can participate in at most one dangling end,
+this is the default for mfe folding but unsupported for the partition
+function folding.
+.IP
+With \fB\-d2\fR this check is ignored, dangling energies will be added for the bases
+adjacent to a helix on both sides in any case; this is the default for
+partition function folding (\fB\-p\fR).
+The option \fB\-d0\fR ignores dangling ends altogether (mostly for debugging).
+With \fB\-d3\fR 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 interior pairs in a loop of degree 3 and works only for mfe
+folding.
+.IP
+Note that by default (as well as with \fB\-d1\fR and \fB\-d3\fR) pf and mfe folding treat
+dangling ends differently. Use \fB\-d2\fR in addition to \fB\-p\fR to ensure that both
+algorithms use the same energy model.
+.TP
+\fB\-\-noLP\fR
+Produce structures without lonely pairs
+(helices of length 1).
+.IP
+(default=off)
+.IP
+For partition function folding this only disallows pairs that can only occur
+isolated. Other pairs may still occasionally occur as helices of length 1.
+.TP
+\fB\-\-noGU\fR
+Do not allow GU pairs
+.IP
+(default=off)
+.TP
+\fB\-\-noClosingGU\fR
+Do not allow GU pairs at the end of helices
+.IP
+(default=off)
+.TP
+\fB\-\-logML\fR
+Recalculate energies of structures using a
+logarithmic energy function for multi\-loops
+before output. (default=off)
+.IP
+This option does not effect structure generation, only the energies that are
+printed out. Since logML lowers energies somewhat, some structures may be
+missing.
+.TP
+\fB\-\-betaScale\fR=\fIDOUBLE\fR
+Set the scaling of the Boltzmann factors
+(default=`1.')
+.IP
+The argument provided with this option enables to scale the thermodynamic
+temperature used in the Boltzmann factors independently from the temperature
+used to scale the individual energy contributions of the loop types. The
+Boltzmann factors then become exp(\fB\-dG\fR/(kT*betaScale)) where k is the
+Boltzmann constant, dG the free energy contribution of the state and T the
+absolute temperature.
+.TP
+\fB\-P\fR, \fB\-\-paramFile\fR=\fIparamfile\fR
+Read energy parameters from paramfile, instead
+of using the default parameter set.
+.IP
+A sample parameter file should accompany your distribution.
+See the RNAlib documentation for details on the file format.
+.TP
+\fB\-\-nsp\fR=\fISTRING\fR
+Allow other pairs in addition to the usual
+AU,GC,and GU pairs.
+.IP
+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 \fB\-nsp\fR \fB\-GA\fR will allow GA and AG pairs. Nonstandard pairs are
+given 0 stacking energy.
+.SH AUTHOR
+
+Ivo L Hofacker, Stefan Wuchty, Walter Fontana, Ronny Lorenz
+.SH REFERENCES
+.I 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
+
+
+S. Wuchty, W. Fontana, I. L. Hofacker and P. Schuster (1999),
+"Complete Suboptimal Folding of RNA and the Stability of Secondary Structures",
+Biopolymers: 49, pp 145-165
+
+.I 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
+.SH "REPORTING BUGS"
+If in doubt our program is right, nature is at fault.
+.br
+Comments should be sent to rna@tbi.univie.ac.at.
git://source.jalview.org / jabaws.git / blobdiff