.TH RNAEFFECTIVE 1
.SH NAME
RNAeffective \- calculation of effective numbers of orthologous miRNA targets
.SH SYNOPSIS
\fBRNAeffective [\-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]
[\fIquery\fB]

.SH DESCRIPTION
.I RNAeffective
is a tool for determining the effective number of orthologous miRNA targets.
This number can be used for the calculation of more accurate joint p-values in
multi-species analyses. RNAeffective searches a set of target sequences with
random miRNAs that can be given on the command line or otherwise generates
random sequences according to given sample size, length distribution parameters
and dinucleotide frequencies. The empirical distribution of joint p-values is
compared to the p-values themselves, and the effective number of independent
targets is the one that reduces the deviation between the two distributions.

.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 22 and
0, 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
queries (either with the \-q option or on command line. If no \-q is given,
the last argument to RNAeffective is taken as a query). See \-q option.
.TP
.B \-q \fIquery_file
Without the \-s option, each of the query sequences in \fIquery_file\fP is
subject to hybridisation with each of the targets (which are from the
\fItarget_file\fP; see \-t below). The sequences in the \fIquery_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 query (or query file) dinucleotide distribution is
counted, and random sequences are generated according to this distribution.

If no \-q is given, random sequences are generated as described above
(see \-d option).
.TP
.B \-t \fItarget_file
See \-q option above.
.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 RNAeffective.

.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, RNAcalibrate