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

NAME

       RNAup - manual page for RNAup 2.5.1

SYNOPSIS

       RNAup [OPTION]...

DESCRIPTION

       RNAup 2.5.1

       Calculate the thermodynamics of RNA-RNA interactions

       RNAup  calculates  the  thermodynamics of RNA-RNA interactions, by decomposing the binding
       into two stages. (1) First the probability that a potential binding sites remains unpaired
       (equivalent  to  the  free  energy  needed  to  open  the site) is computed. (2) Then this
       accessibility is combined with the interaction energy to obtain the total binding  energy.
       All   calculations   are   done   by  computing  partition  functions  over  all  possible
       conformations.

       RNAup provides two different modes: By default RNAup computes accessibilities, in terms of
       the  free  energies  needed  to  open a region (default length 4). It prints the region of
       highest accessibility and its opening energy to stdout, opening  energies  for  all  other
       regions are written to a file.

       In  interaction  mode the interaction between two RNAs is calculated. It is invoked if the
       input consists of two sequences concatenated with an "&", or if the options -X[pf]  or  -b
       are  given.  Unless  the  -b  option  is  specified RNAup assumes that the longer RNA is a
       structured target sequence while the shorter one is an unstructured small RNA.
       Additionally, for every position along the target sequence we write the best  free  energy
       of  binding for an interaction that includes this position to the the output file.  Output
       to stdout consists of the location  and  free  energy,  dG,  for  the  optimal  region  of
       interaction.  The  binding  energy  dG  is  also split into its components the interaction
       energy dGint and the opening energy dGu_l (and possibly dGu_s for the shorter sequence).
       In addition we print the optimal interaction structure as computed by RNAduplex  for  this
       region.  Note  that it can happen that the RNAduplex computed optimal interaction does not
       coincide with the optimal RNAup region. If the two predictions don't match  the  structure
       string is replaced by a run of "."  and a message is written to stderr.

       Each  sequence  should  be in 5' to 3' direction. If the sequence is preceded by a line of
       the form
       > name

       the output file "name_ux_up.out" is produced, where the "x" in "ux" is the  value  set  by
       the  -u  option.  Otherwise  the  file  name  defaults  to  RNA_ux_up.out.  The  output is
       concatenated if a file with the same name exists.

       RNA sequences are read from stdin as strings of characters. White space and newline within
       a  sequence  cause  an  error!  Newline  is  used  to separate sequences. The program will
       continue to read new sequences until a line consisting of the single character @ or an end
       of file condition is encountered.

       -h, --help
              Print help and exit

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

       --full-help
              Print help, including hidden options, and exit

       -V, --version
              Print version and exit

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

       -C, --constraint
              Apply structural constraint(s) during prediction.  (default=off)

              The  program first reads the sequence(s), then a dot-bracket like string containing
              constraints on the structure. The following symbols are recognized:

              '.' ... no constraint for this base

              'x' ... the base is unpaired

              '<' ... the base pairs downstream, i.e. i is paired with j > i

              '>' ... the base pairs upstream, i.e. i is paired with j < i

              '()' ... base i pairs with base j

              '|' ... the corresponding base has to be paired intermolecularily (only for

              interaction mode)

       -o, --no_output_file
              Do not produce an output file.  (default=off)

       --no_header
              Do not produce a header with the command line parameters used  in  the  outputfile.
              (default=off)

       --noconv
              Do not automatically substitude nucleotide "T" with "U".  (default=off)

   Calculations of opening energies:
       -u, --ulength=length
              Specify the length of the unstructured region in the output.  (default=`4')

              The  probability  of  being unpaired is plotted on the right border of the unpaired
              region. You can specify up to 20 different length values:  use  "-"  to  specify  a
              range  of  continuous  values  (e.g.  -u  4-8) or specify a list of comma separated
              values (e.g. -u 4,8,15).

       -c, --contributions=SHIME
              Specify the contributions listed in the output.  (default=`S')

              By default only the full probability of being unpaired is plotted.  The  -c  option
              allows  one  to  get  the  different  contributions (c) to the probability of being
              unpaired: The full probability of being unpaired ("S" is the sum of the probability
              of  being  unpaired in the exterior loop ("E"), within a hairpin loop ("H"), within
              an interior loop ("I") and within a  multiloop  ("M").  Any  combination  of  these
              letters may be given.

   Calculations of RNA-RNA interactions:
       -w, --window=INT
              Set the maximal length of the region of interaction.  (default=`25')

       -b, --include_both
              Include the probability of unpaired regions in both (b) RNAs.  (default=off)

              By  default  only  the  probability of being unpaired in the longer RNA (target) is
              used.

       -5, --extend5=INT
              Extend the region of interaction in the target to some residues on the 5' side.

              The underlying assumption is that it is favorable for an interaction  if  not  only
              the direct region of contact is unpaired but also a few residues 5'

       -3, --extend3=INT
              Extend the region of interaction in the target to some residues on the 3' side.

              The  underlying  assumption  is that it is favorable for an interaction if not only
              the direct region of contact is unpaired but also a few residues 3'

       --interaction_pairwise
              Activate pairwise interaction mode.  (default=off)

              The first sequence interacts  with  the  2nd,  the  third  with  the  4th  etc.  If
              activated, two interacting sequences may be given in a single line separated by "&"
              or each sequence may be given on an extra line.

       --interaction_first
              Activate interaction mode using first sequence only.  (default=off)

              The  interaction  of  each  sequence  with  the  first  one  is  calculated   (e.g.
              interaction  of one mRNA with many small RNAs). Each sequence has to be given on an
              extra line

   Model Details:
       -S, --pfScale=DOUBLE
              Set scaling factor for Boltzmann factors to prevent under/overflows.

              In the calculation of the pf use scale*mfe as an estimate  for  the  ensemble  free
              energy  (used  to  avoid  overflows). The default is 1.07, useful values are 1.0 to
              1.2. Occasionally needed for long sequences.  You can also recompile the program to
              use double precision (see the README file).

       -T, --temp=DOUBLE
              Rescale energy parameters to a temperature in degrees centigrade.  (default=`37.0')

       -4, --noTetra
              Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop
              hairpins.  (default=off)

              Mostly for testing.

       -d, --dangles=INT
              Specify "dangling end" model for  bases  adjacent  to  helices  in  free  ends  and
              multi-loops.  (default=`2')

              With  -d2 dangling energies will be added for the bases adjacent to a helix on both
              sides in any case.

              The option -d0 ignores dangling ends altogether (mostly for debugging).

       --noLP Produce structures without lonely pairs (helices of length 1).  (default=off)

              For partition function folding this  only  disallows  pairs  that  can  only  occur
              isolated. Other pairs may still occasionally occur as helices of length 1.

       --noGU Do not allow GU pairs.  (default=off)

       --noClosingGU
              Do not allow GU pairs at the end of helices.  (default=off)

       -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.

       --nsp=STRING
              Allow other pairs in addition to the usual AU,GC,and GU pairs.

              Its argument is a comma separated list of additionally allowed pairs. If the  first
              character  is  a  "-"  then  AB  will imply that AB and BA are allowed pairs.  e.g.
              RNAfold -nsp -GA  will allow GA  and  AG  pairs.  Nonstandard  pairs  are  given  0
              stacking energy.

       -e, --energyModel=INT
              Set energy model.

              Rarely  used option to fold sequences from the artificial ABCD... alphabet, where A
              pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.

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

       U. Mueckstein, H. Tafer, J. Hackermueller, S.H. Bernhart, P.F. Stadler, and I.L.  Hofacker
       (2006), "Thermodynamics of RNA-RNA Binding", Bioinformatics: 22(10), pp 1177-1182

       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

EXAMPLES

       Output to stdout:

       In Interaction mode RNAup prints the most favorable interaction  energy  between  the  two
       sequences to stdout. The most favorable interaction energy (dG) depends on the position in
       the longer sequence (region [i,j]) and the position in the shorter sequence (region[k,l]):
       dG[i,j;k,l].   dG[i,j;k,l]  is  the  largest  contribution to dG[i,j] = sum_kl dG[i,j;k,l]
       which is given in the output file: therefore dG[i,j;k,l] <= dG[i,j].

         '....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8'
         > franz
         GGAGUAGGUUAUCCUCUGUU
         > sissi
         AGGACAACCU
         dG = dGint + dGu_l
         (((((.((((&)))).)))))   6,15  :   1,10  (-6.66 = -9.89 + 3.23)
         AGGUUAUCCU&AGGACAACCU
         RNAup output in file: franz_sissi_w25_u3_4_up.out

       where the result line contains following information

         RNAduplex results       [i,j]     [k,l]    dG = dGint + dGu_l
         (((((.((((&)))).)))))   6,15   :  1,10     (-6.66=-9.89+3.23)

       Output to file:

       Output to file contains a header including date, the command line of the  call  to  RNAup,
       length  and names of the input sequence(s) followed by the sequence(s). The first sequence
       is the target sequence.  Printing of the header can be turned off using the -nh option.

       The line directly after the header gives the column names for the output:

         position     dGu_l for -u 3      dGu_l for -u 4       dG
       #     pos      u3S       u3H       u4S       u4H        dG

       where all information refers to the target sequence. The dGu_l column contains information
       about  the  -u  value  (u=3  or  u=4)  and the contribution to the free energy to open all
       structures "S" or only hairpin loops "H", see option -c.  NA  means  that  no  results  is
       possible (e.g. column u3S row 2: no region of length 3 ending at position 2 exists).

       #  Thu Apr 10 09:15:11 2008
       #  RNAup -u 3,4 -c SH -b
       #  20 franz
       #  GGAGUAGGUUAUCCUCUGUU
       #  10 sissi
       #  AGGACAACCU
       #     pos      u3S       u3H       u4S       u4H        dG
              1        NA        NA        NA        NA    -1.540
              2        NA        NA        NA        NA    -1.540
              3     1.371        NA        NA        NA    -1.217
              4     1.754     5.777     1.761        NA    -1.393
              5     1.664     3.140     1.811     5.800    -1.393

       If  the  -b  option  is  selected  position  and dGu_s values for the shorter sequence are
       written after the information for the target sequence.

AUTHOR

       Ivo L Hofacker, Peter F Stadler, Ulrike Mueckstein, Ronny Lorenz

REPORTING BUGS

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