Ubuntu Manpage: RNAhybrid - calculate secondary structure hybridisations of RNAs

NAME

       RNAhybrid - calculate secondary structure hybridisations of RNAs

SYNOPSIS

       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]

DESCRIPTION

       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.

OPTIONS

-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.

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

       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

VERSION

       This man page documents version 2.0 of RNAhybrid.

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.

BUGS

       In suboptimal hits, dangling ends appear  as  Ns  if  they  were  in  the  first  or  last
       hybridising position of a previous hit.