NAME
RNAeffective - calculation of effective numbers of orthologous miRNA
targets
SYNOPSIS
RNAeffective [-h] [-d frequency_file] [-f from,to] [-k sample_size] [-l
mean,std] [-m max_target_length] [-n max_query_length] [-u
iloop_upper_limit] [-v bloop_upper_limit] [-s] [-t target_file] [-q
query_file] [query]
DESCRIPTION
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.
OPTIONS
-h Give a short summary of command line options.
-d frequency_file
Generate random sequences according to dinucleotide frequencies
given in frequency_file. See example directory for example
files.
-f from,to
Forces all structures to have a helix from position from to
position to with respect to the query. The first base has
position 1.
-k sample_size
Generate sample_size random sequences. Default value is 5000.
-l mean,std
Generate random sequences with a normal length distribution of
mean mean and standard deviation std. Default values are 22 and
0, respectively.
-m max_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).
-n max_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).
-u iloop_upper_limit
The maximally allowed number of unpaired nucleotides in either
side of an internal loop.
-v bloop_upper_limit
The maximally allowed number of unpaired nucleotides in a bulge
loop.
-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.
-q query_file
Without the -s option, each of the query sequences in query_file
is subject to hybridisation with each of the targets (which are
from the target_file; see -t below). The sequences in the
query_file 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).
-t target_file
See -q option above.
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
VERSION
This man page documents version 2.0 of RNAeffective.
AUTHORS
Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann.
LIMITATIONS
Character dependent energy values are only defined for [acgtuACGTU].
All other characters lead to values of zero in these cases.
SEE ALSO
RNAhybrid, RNAcalibrate