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.