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)