.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH VIENNARNA "1" "April 2013" "ViennaRNA Package 2.1.1" "RNAcop"
.SH NAME
ViennaRNA \- RNAcop
.SH SYNOPSIS
.B ViennaRNA
[\fIOPTIONS\fR]...
.SH DESCRIPTION
ViennaRNA 1.0
.PP
Find optimal flanking regions for a desired structure motif
.PP
Reads in a sequence and a structures constraint containing a desired
substructure.Computes the subsequence that maximizes the probability that the
constraint is fullfilled,i.e. that the desired structure is formed.
.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 "Program specific Options:"
.IP
Below are command line options specific for RNAcop
.TP
\fB\-\-minleft\fR=\fIINT\fR
Minimum size of flanking region to the left of
the structure motif.
.TP
\fB\-\-minright\fR=\fIINT\fR
Minimum size of flanking region to the right of
the structure motf.
.TP
\fB\-\-maxleft\fR=\fIINT\fR
Maximum size of flanking region to the left of
the structure motif.
.TP
\fB\-\-maxright\fR=\fIINT\fR
Minimum size of flanking region to the right of
the structure motif.
.TP
\fB\-\-minlen\fR=\fIINT\fR
Minimum total length of the subssequence.
.TP
\fB\-\-full\fR
Print all pairwise combinations for ddG values
to STDOUT.
.IP
(default=off)
.SS "General Options:"
.IP
Below are command line options which alter the general behavior of this
program
.TP
\fB\-\-noconv\fR
Do not automatically substitude nucleotide
"T" with "U"
.IP
(default=off)
.TP
\fB\-\-noPS\fR
Do not produce postscript drawing of the mfe
structure.
.IP
(default=off)
.TP
\fB\-c\fR, \fB\-\-circ\fR
Assume a circular (instead of linear) RNA
molecule.
.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')
.TP
\fB\-\-noLP\fR
Produce structures without lonely pairs
(helices of length 1).
.IP
(default=off)
.TP
\fB\-\-noGU\fR
Do not allow GU pairs
(default=off)
.TP
\fB\-\-noClosingGU\fR
Do not allow GU pairs at the end of helices
(default=off)
.TP
\fB\-P\fR, \fB\-\-paramFile\fR=\fIparamfile\fR
Read energy parameters from paramfile, instead
of using the default parameter set.
.PP
If in doubt our program is right, nature is at fault.
Comments should be sent to rna@tbi.univie.ac.at.
.SH "SEE ALSO"
The full documentation for
.B ViennaRNA
is maintained as a Texinfo manual.  If the
.B info
and
.B ViennaRNA
programs are properly installed at your site, the command
.IP
.B info ViennaRNA
.PP
should give you access to the complete manual.
