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.