RNAEFFECTIVE(1) General Commands Manual RNAEFFECTIVE(1)
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 dinu-
cleotide 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
RNAEFFECTIVE(1)