xenial (1) RNAhybrid.1.gz

Provided by: rnahybrid_2.1.2-1_amd64 bug

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.

SEE ALSO

       RNAcalibrate, RNAeffective

                                                                                                    RNAHYBRID(1)