Provided by: rnahybrid_2.1.2-5_amd64 bug


       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


       -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

       -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