--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNADUPLEX "1" "July 2013" "RNAduplex 2.1.2" "User Commands"
+.SH NAME
+RNAduplex \- manual page for RNAduplex 2.1.2
+.SH SYNOPSIS
+.B RNAduplex
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAduplex 2.1.2
+.PP
+Compute the structure upon hybridization of two RNA strands
+.PP
+reads two RNA sequences from stdin or <filename> and computes optimal and
+suboptimal secondary structures for their hybridization. The calculation is
+simplified by allowing only inter\-molecular base pairs, for the general case
+use RNAcofold.
+The computed optimal and suboptimal structure are written to stdout, one
+structure per line. Each line consist of: The structure in dot bracket format
+with a "&" separating the two strands. The range of the structure in the two
+sequences in the format "from,to : from,to"; the energy of duplex structure
+in kcal/mol.
+The format is especially useful for computing the hybrid structure between a
+small probe sequence and a long target sequence.
+.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\-s\fR, \fB\-\-sorted\fR
+sort the printed output by free energy
+.IP
+(default=off)
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide "T"
+with "U"
+.IP
+(default=off)
+.SS "Algorithms:"
+.IP
+Select additional algorithms which should be included in the calculations.
+.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.
+.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\-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, 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
+
+
+.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.
+.SH "SEE ALSO"
+
+RNAcofold(l) RNAfold(l)
git://source.jalview.org / jabaws.git / blobdiff