NAME

       RNAcalibrate - calibrate statistics of secondary structure hybridisations of RNAs

SYNOPSIS

       RNAcalibrate  [-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]
       [target] [query]

DESCRIPTION

       RNAcalibrate is a tool for calibrating minimum free energy (mfe) hybridisations performed with RNAhybrid.
       It searches a random database that can be given  on  the  command  line  or  otherwise  generates  random
       sequences according to given sample size, length distribution parameters and dinucleotide frequencies. To
       the empirical distribution of length normalised minimum free energies, parameters  of  an  extreme  value
       distribution  (evd)  are  fitted.  The  output gives for each miRNA its name (or "command_line" if it was
       submitted on the command line), the number of data points the evd fit was done on, the location  and  the
       scale  parameter.  The  location  and  scale parameters of the evd can then be given to RNAhybrid for the
       calculation of mfe p-values.

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 500 and 300, 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 targets (either with
              the -t option or on command line. If no -t is given, either the last argument (if a -q  is  given)
              or  the  second  last  argument  (if no -q is given) to RNAcalibrate is taken as a target). See -t
              option.

       -t target_file
              Without the -s option, each of the target sequences in target_file  is  subject  to  hybridisation
              with  each  of  the  queries  (which  either  are from the query_file or is the one query given on
              command line; see -q below). The sequences in the target_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 target (or target file) dinucleotide distribution is counted,  and  random
              sequences are generated according to this distribution.

              If no -t is given, random sequences are generated as described above (see -d option).

       -q query_file
              See -t option above. If no -q is given, the last argument to RNAcalibrate is taken as a query.

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 RNAcalibrate.

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, RNAeffective

                                                                                                 RNACALIBRATE(1)