SYNOPSISRNAcalibrate [-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]
DESCRIPTIONRNAcalibrate 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.
- 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.
- 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.
REFERENCESThe 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
VERSIONThis man page documents version 2.0 of RNAcalibrate.
AUTHORSMarc Rehmsmeier, Peter Steffen, Matthias Hoechsmann.
LIMITATIONSCharacter dependent energy values are only defined for [acgtuACGTU]. All other characters lead to values of zero in these cases.