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.
RNAhybrid, RNAcalibrate