Provided by: vienna-rna_2.5.1+dfsg-1_amd64 bug

NAME

       RNAplex - manual page for RNAplex 2.5.1

SYNOPSIS

       RNAplex [options]

DESCRIPTION

       RNAplex 2.5.1

       Find targets of a query RNA

       reads  two  RNA  sequences  from  stdin  or <filename> and computes optimal and suboptimal
       secondary structures for their hybridization. The calculation is  simplified  by  allowing
       only  inter-molecular  base  pairs. Accessibility effects can be estimated by RNAplex if a
       RNAplfold  accessibility  profile  is  provided.   The  computed  optimal  and  suboptimal
       structure  are  written  to  stdout,  one  structure  per  line. Each line consist of: The
       structure in dot bracket format with a "&" separating the two strands. The  range  of  the
       structure  in  the  two sequences in the format  "from,to : from,to"; the energy of duplex
       structure in kcal/mol.  The format is especially useful for computing the hybrid structure
       between a small probe sequence and a long target sequence.

       -h, --help
              Print help and exit

       --detailed-help
              Print help, including all details and hidden options, and exit

       --version
              Print version and exit

   Input Options:
              Below  are  command  line  options  which  alter the general input behavior of this
              program

       -q, --query=STRING
              File containing the query sequence.

              Input sequences can be given piped to RNAplex or given in a query file with the  -q
              option. Note that the -q option implies that the -t option is also used

       -t, --target=STRING
              File containing the target sequence.

              Input sequences can be given piped to RNAplex or given in a target file with the -t
              option. Note that the -t option implies that the -q option is also used

       -a, --accessibility-dir=STRING
              Location of the accessibility profiles.

              This option switches the accessibility modes on and indicates  in  which  directory
              accessibility profiles as generated by RNAplfold can be found

       -b, --binary
              Allow the reading and parsing of memory dumped opening energy file

              (default=off)

              The  -b  option allows one to read and process opening energy files which are saved
              in binary format

              This can reduce by a factor of 500x-1000x the time needed to process those

              files. RNAplex recognizes the corresponding opening energy  files  by  looking  for
              files  named after the sequence and containing the suffix _openen_bin.  Please look
              at the man page of RNAplfold if you need more information on how to produce  binary
              opening energy files.

       -P, --paramFile=paramfile
              Read energy parameters from paramfile, instead of using the default parameter set.

              Different  sets  of  energy  parameters  for  RNA  and  DNA  should  accompany your
              distribution.  See the RNAlib documentation for details on the  file  format.  When
              passing the placeholder file name "DNA", DNA parameters are loaded without the need
              to actually specify any input file.

   Algorithms:
              Options which alter the computing behaviour of RNAplex.

       -T, --temp=DOUBLE
              Rescale energy parameters to a temperature T.  Default is 37C.

       -l, --interaction-length=INT
              Maximal length of an interaction (default=`40')

              Maximal allowed length of an interaction

       -c, --extension-cost=INT
              Cost to add to each nucleotide in a duplex (default=`0')

              Cost of extending a duplex by one nucleotide. Allows one to find compact  duplexes,
              having  few/small  bulges  or  interior  loops  Only  useful  when no accessibility
              profiles are available. This option is disabled if accessibility profiles are  used
              (-a option)

       -p, --probe-mode
              Compute Tm for probes  (default=off)

              Use this option if you want to compute the melting temperature of your probes

       -Q, --probe-concentration=DOUBLE
              Set the probe concentration for the Tm

              computation

              (default=`0.1')

       -N, --na-concentration=DOUBLE Set the Na+ concentration for the Tm
              computation

              (default=`1.0')

       -M, --mg-concentration=DOUBLE Set the Mg2+ concentration for the Tm
              computation

              (default=`1.0')

       -K, --k-concentration=DOUBLE
              Set the K+ concentration for the Tm computation

              (default=`1.0')

       -U, --tris-concentration=DOUBLE
              Set the tris+ concentration for the Tm

              computation

              (default=`1.0')

       -f, --fast-folding=INT
              Speedup of the target search (default=`0')

              This option allows one to decide if the backtracking has to be done (-f 0, -f 2) or
              not (-f 1). For -f 0 the structure is computed based on the standard energy  model.
              This  is  the slowest and most precise mode of RNAplex. With -f 2, the structure is
              computed based on the approximated plex model. If a lot  of  targets  are  returned
              this  is  can greatly improve the runtime of RNAplex.  -f 1 is the fastest mode, as
              no structure are recomputed

       -V, --scale-accessibility=DOUBLE
              Rescale all opening energy by a factor V

              (default=`1.0')

              Scale-factor for the accessibility. If V is set to 1 then the scaling has no effect
              on the accessibility.

       -C, --constraint
              Calculate structures subject to constraints.  (default=off)

              The  program  reads first the sequence, then a string containing constraints on the
              structure for the query sequence encoded with the symbols:  .  (no  constraint  for
              this base) | (the corresponding base has to be paired)

       -A, --alignment-mode
              Tells RNAplex to compute interactions based on alignments

              (default=off)

              If  the  A  option is set RNAplex expects clustalw files as input for the -q and -t
              option.

       -k, --convert-to-bin
              If set, RNAplex will convert all opening energy file in a directory set by  the  -a
              option into binary opening energy files

              (default=off)

              RNAplex  can  be  used to convert existing text formatted opening energy files into
              binary formatted files. In this mode RNAplex does not compute interactions.

   Output:
              Options that modify the output

       -z, --duplex-distance=INT
              Distance between target 3' ends of two consecutive duplexes

              (default=`0')

              Distance between the target 3'ends of two consecutive duplexes. Should  be  set  to
              the maximal length of interaction to get good results

              Smaller z leads to larger overlaps between consecutive duplexes.

       -e, --energy-threshold=DOUBLE Minimal energy for a duplex to be returned
              (default=`-100000')

              Energy  threshold  for  a  duplex to be returned. The threshold is set on the total
              energy of interaction, i.e. the hybridization energy corrected for  opening  energy
              if -a is set or the energy corrected by -c. If unset, only the mfe will be returned

       -I, --produce-ps=STRING
              Draw an alignment annotated interaction from RNAplex

              This option allows one to produce interaction figures in PS-format a la RNAalifold,
              where base-pair conservation is represented in color-coded format. In this mode  no
              interaction  are  computed,  but  the  -I option indicates the location of the file
              containing interactions between two RNA (alignments/sequence) from a previous  run.
              If  the  -A  option  is  not  set  a structure figure a la RNAfold with color-coded
              annotation of the accessibilities is returned

       -L, --WindowLength=INT
              Tells how large the region around the target  site  should  be  for  redrawing  the
              alignment interaction

              (default=`1')

              This  option allows one to specify how large the region surrounding the target site
              should be set when generating the alignment figure of the interaction

REFERENCES

       If you use this program in your work you might want to cite:

       R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler  and
       I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26

       I.L.  Hofacker,  W.  Fontana,  P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994),
       "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125,  pp
       167-188

       R.  Lorenz,  I.L.  Hofacker,  P.F.  Stadler  (2016),  "RNA  folding  with  hard  and  soft
       constraints", Algorithms for Molecular Biology 11:1 pp 1-13

       The calculation of duplex structure is based on dynamic programming  algorithm  originally
       developed by Rehmsmeier and in parallel by Hofacker.

       H. Tafer and I.L. Hofacker (2008), "RNAplex: a fast tool for RNA-RNA interaction search.",
       Bioinformatics: 24(22), pp 2657-2663

       S. Bonhoeffer, J.S. McCaskill, P.F. Stadler,  P.  Schuster  (1993),  "RNA  multi-structure
       landscapes", Euro Biophys J: 22, pp 13-24

       The energy parameters are taken from:

       D.H.  Mathews,  M.D.  Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker,
       D.H. Turner (2004),  "Incorporating  chemical  modification  constraints  into  a  dynamic
       programming  algorithm  for prediction of RNA secondary structure", Proc. Natl. Acad. Sci.
       USA: 101, pp 7287-7292

       D.H Turner, D.H. Mathews (2009),  "NNDB:  The  nearest  neighbor  parameter  database  for
       predicting  stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp
       280-282

AUTHOR

       Hakim Tafer, Ivo L. Hofacker

REPORTING BUGS

       If in doubt our program is right,  nature  is  at  fault.   Comments  should  be  sent  to
       rna@tbi.univie.ac.at.