.TH RNACALIBRATE 1
.SH NAME
RNAcalibrate \- calibrate statistics of secondary structure hybridisations of
RNAs
.SH SYNOPSIS
\fBRNAcalibrate [\-h] [\-d \fIfrequency_file\fB] [\-f \fIfrom,to\fB] [\-k
\fIsample_size\fB] [\-l \fImean,std\fB] [\-m \fImax_target_length\fB] [\-n
\fImax_query_length\fB] [\-u \fIiloop_upper_limit\fB] [\-v
\fIbloop_upper_limit\fB] [\-s] [\-t \fItarget_file\fB] [\-q \fIquery_file\fB]
[\fItarget\fB] [\fIquery\fB]

.SH DESCRIPTION
.I RNAcalibrate
is a tool for calibrating minimum free energy (mfe) hybridisations performed
with RNAhybrid. It searches a random database that can be given on the command
line or otherwise generates random sequences according to given sample size,
length distribution parameters and dinucleotide frequencies. To the empirical
distribution of length normalised minimum free energies, parameters of an
extreme value distribution (evd) are fitted. The output gives for each miRNA
its name (or "command_line" if it was submitted on the command line), the
number of data points the evd fit was done on, the location and the scale
parameter. The location and scale parameters of the evd can then be given to
RNAhybrid for the calculation of mfe p-values.

.SH OPTIONS
.TP
.B \-h
Give a short summary of command line options.
.TP
.B \-d \fIfrequency_file
Generate random sequences according to dinucleotide frequencies
given in \fIfrequency_file\fP. See example directory for example
files.
.TP
.B \-f \fIfrom,to
Forces all structures to have a helix from position \fIfrom\fP to position
\fIto\fP with respect to the query. The first base has position 1.
.TP
.B \-k \fIsample_size
Generate \fIsample_size\fP random sequences. Default value is 5000.
.TP
.B \-l \fImean,std
Generate random sequences with a normal length distribution of
mean \fImean\fP and standard deviation \fIstd\fP. Default values are 500 and
300, respectively.
.TP
.B \-m \fImax_target_length
The maximum allowed length of a target sequence. The default value is
2000. This option only has an effect if a target file is given with the \-t
option (see below).
.TP
.B \-n \fImax_query_length
The maximum allowed length of a query sequence. The default value is 30. This
option only has an effect if a query file is given with the \-q option (see
below).
.TP
.B \-u \fIiloop_upper_limit
The maximally allowed number of unpaired nucleotides in either side of an
internal loop.
.TP
.B \-v \fIbloop_upper_limit
The maximally allowed number of unpaired nucleotides in a bulge loop.
.TP
.B \-s
Generate random sequences according to the dinucleotide distribution of given
targets (either with the \-t option or on command line. If no \-t is given,
either the last argument (if a \-q is given) or the second last argument (if no
\-q is given) to RNAcalibrate is taken as a target). See \-t option.
.TP
.B \-t \fItarget_file
Without the \-s option, each of the target sequences in \fItarget_file\fP is
subject to hybridisation with each of the queries (which either are from the
\fIquery_file\fP or is the one query given on command line; see \-q below). The
sequences in the \fItarget_file\fP have to be in FASTA format, ie. one line
starting with a \> and directly followed by a name, then one or more following
lines with the sequence itself. Each individual sequence line must not have
more than 1000 characters.

With the \-s option, the target (or target file) dinucleotide distribution is
counted, and random sequences are generated according to this distribution.

If no \-t is given, random sequences are generated as described above
(see \-d option).
.TP
.B \-q \fIquery_file
See \-t option above. If no \-q is given, the last argument to RNAcalibrate is
taken as a query.
.SH REFERENCES
The energy parameters are taken from:

Mathews DH, Sabina J, Zuker M, Turner DH.
"Expanded sequence dependence of thermodynamic parameters improves 
prediction of RNA secondary structure"
J Mol Biol., 288 (5), pp 911-940, 1999

.SH VERSION
This man page documents version 2.0 of RNAcalibrate.

.SH AUTHORS
Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann.

.SH LIMITATIONS
Character dependent energy values are only defined for [acgtuACGTU].
All other characters lead to values of zero in these cases.

.SH SEE ALSO
RNAhybrid, RNAeffective