RNAeffective - calculation of effective numbers of orthologous
miRNA targets
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]
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.
- -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.
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
This man page documents version 2.0 of RNAeffective.
Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann.
Character dependent energy values are only defined for
[acgtuACGTU]. All other characters lead to values of zero in these
cases.