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)