Ubuntu Manpage: RNAeffective - calculation of effective numbers of orthologous miRNA targets

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.