RNAhybrid - calculate secondary structure hybridisations of RNAs
RNAhybrid [-h] [-b hit_number] [-e energy_cutoff]
[-p p-value_cutoff] [-c] [-d xi,theta] [-s
set_name] [-f from,to] [-m
max_target_length ] [-n max_query_length] [-u
iloop_upper_limit] [-v bloop_upper_limit] [-g
(ps|png|jpg|all)] [-t target_file] [-q
query_file ] [target] [query]
RNAhybrid is a tool for finding minimum free energy (mfe) hybridisations
of a long (target) and a short (query) RNA. The hybridisation is performed in
a kind of domain mode, ie. the short sequence is hybridised to the best
fitting parts of the long one. The tool is primarily meant as a means for
microRNA target prediction. In addition to mfes, the program calculates
p-values based on extreme value distributions of length normalised energies.
- -h
- Give a short summary of command line options.
- -b hit_number
- Maximal number of hits to show. hit_number hits with
increasing minimum free energy (reminder: larger energies are worse) are
shown, unless the -e option is used and the energy cut-off has been
exceeded (see -e option below) or there are no more hits. Hits may only
overlap at dangling bases (5' or 3' unpaired end of target).
- -c
- Produce compact output. For each target/query pair one line
of output is generated. Each line is a colon (:) separated list of the
following fields: target name, query name, minimum free energy, position
in target, alignment line 1, line 2, line 3, line 4. If a target or a
query is given on command line (ie. no -t or -q respectively), its name in
the output will be "command line".
- -d xi,theta
- xi and theta are the position and shape parameters,
respectively, of an extreme value distribution (evd). p-values of duplex
energies are assumed to be distributed according to such an evd. For a
length normalised energy en, we have P[X <= en] = 1 -
exp(-exp(-(-en-xi)/theta)), where en = e/log(m*n) with m and n being the
lengths of the target and the query, respectively. If the -d option is
omitted, xi and theta are estimated from the maximal duplex energy of the
query, assuming a linear dependence. The parameters of this linear
dependence are coded into the program, but the option -s has to be given
to choose from the appropriate set. Note that the evd is mirrored, since
good mfes are large negative values.
- -s set_name
- Used for quick estimate of extreme value distribution
parameters (see -d option above). Tells RNAhybrid which target dataset to
assume. Valid parameters are 3utr_fly, 3utr_worm and 3utr_human.
- -e energy_cutoff
- Hits with increasing minimum free energy (reminder: larger
energies are worse) less than or equal to energy_cutoff are shown,
unless the -b option is used and the number of already reported hits has
reached the maximal hit_number (see -b option above). Hits may only
overlap at dangling bases (5' or 3' unpaired end of target).
- -p p-value_cutoff
- Only hits with p-values not larger than
p-value_cutoff are reported. See also options -d and -s.
- -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.
- -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.
- -g (ps|png|jpg|all)
- Produce a plot of the hybridisation, either in ps, png or
jpg format, or for all formats together. The plots are saved in files
whose names are created from the target and query names
("command_line" if given on the command line). This option only
works, if the appropriate graphics libraries are present.
- -t target_file
- 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. 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 RNAhybrid is taken as a target.
- -q query_file
- See -t option above.
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
The graphical output uses code from the Vienna RNA package:
Hofacker IL. "Vienna RNA secondary structure server." Nucleic Acids
Research, 31 (13), pp 3429-3431, 2003
This man page documents version 2.0 of RNAhybrid.
Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann.
Character dependent energy values are only defined for [acgtuACGTU]. All other
characters lead to values of zero in these cases.
In suboptimal hits, dangling ends appear as Ns if they were in the first or last
hybridising position of a previous hit.
RNAcalibrate, RNAeffective