--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAINVERSE "1" "July 2013" "RNAinverse 2.1.2" "User Commands"
+.SH NAME
+RNAinverse \- manual page for RNAinverse 2.1.2
+.SH SYNOPSIS
+.B RNAinverse
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAinverse 2.1.2
+.PP
+Find RNA sequences with given secondary structure
+.PP
+The program searches for sequences folding into a predefined structure, thereby
+inverting the folding algorithm. Target structures (in bracket notation) and
+starting sequences for the search are read alternately from stdin.
+Characters in the start sequence other than "AUGC" (or the alphabet specified
+with \fB\-a\fR) will be treated as wild cards and replaced by a random character. Any
+lower case characters in the start sequence will be kept fixed during the
+search. If necessary, the sequence will be elongated to the length of the
+structure. Thus a string of "N"s as well as a blank line specify a random
+start sequence.
+For each search the best sequence found and its Hamming distance to the start
+sequence are printed to stdout. If the the search was unsuccessful, a structure
+distance to the target is appended.
+The \fB\-Fp\fR and \fB\-R\fR options can modify the output format, see commandline options
+below.
+The program will continue to read new structures and sequences until a line
+consisting of the single character "@" or an end of file condition is
+encountered.
+.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\-R\fR, \fB\-\-repeat\fR[=\fIINT\fR]
+Search repeatedly for the same structure.
+If an argument is supplied to this option it
+must follow the option flag immediately. E.g.:
+\fB\-R5\fR
+.IP
+(default=`100')
+.IP
+If repeats is negative search until \fB\-\-repeats\fR exact solutions are found, no
+output is done for unsuccessful searches. Be aware, that the program will not
+terminate if the target structure can not be found.
+If no value is supplied with this option, the default value is used.
+.TP
+\fB\-a\fR, \fB\-\-alphabet\fR=\fIALPHABET\fR
+Find sequences using only nucleotides from a given
+alphabet.
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+In conjunction with a negative value supplied to
+\fB\-R\fR, print the last subsequence and substructure
+for each unsuccessful search.
+.IP
+(default=off)
+.SS "Algorithms:"
+.IP
+Select additional algorithms which should be included in the calculations.
+.TP
+\fB\-F\fR, \fB\-\-function\fR=\fImp\fR
+Use minimum energy (\fB\-Fm\fR), partition function
+folding (\fB\-Fp\fR) or both (\fB\-Fmp\fR).
+.IP
+(default=`m')
+.IP
+In partition function mode, the probability of the target structure
+exp(\fB\-E\fR(S)/kT)/Q is maximized. This probability is written in brackets after
+the found sequence and Hamming distance. In most cases you'll want to use the
+\fB\-f\fR option in conjunction with \fB\-Fp\fR, see below.
+.TP
+\fB\-f\fR, \fB\-\-final\fR=\fIFLOAT\fR
+In combination with \fB\-Fp\fR stop search when sequence
+is found with E(s)\-F is smaller than final,
+where F=\-kT*ln(Q).
+.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 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\-Fp\fR to ensure that both
+algorithms use the same energy model.
+.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\-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.
+.TP
+\fB\-e\fR, \fB\-\-energyModel\fR=\fIINT\fR
+Rarely used option to fold sequences from the
+artificial ABCD... alphabet, where A pairs B,
+C\-D etc. Use the energy parameters for GC (\fB\-e\fR
+1) or AU (\fB\-e\fR 2) pairs.
+.SH EXAMPLES
+To search 5 times for sequences forming a simple hairpin structure interrupted by one GA mismatch call
+
+.nf
+.ft CW
+ $ RNAinverse -R 5
+.ft
+.fi
+
+
+and enter the lines
+
+.nf
+.ft CW
+ (((.(((....))).)))
+ NNNgNNNNNNNNNNaNNN
+.ft
+.fi
+.SH AUTHOR
+
+Ivo L Hofacker
+.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
+
+
+D.H. Turner, N. Sugimoto, S.M. Freier (1988),
+"RNA structure prediction",
+Ann Rev Biophys Biophys Chem: 17, pp 167-192
+
+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 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.
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