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

NAME

       RNAplfold - manual page for RNAplfold 2.5.1

SYNOPSIS

       RNAplfold [OPTION]...

DESCRIPTION

       RNAplfold 2.5.1

       calculate locally stable secondary structure - pair probabilities

       Computes  local  pair  probabilities  for  base  pairs  with  a  maximal  span  of  L. The
       probabilities are averaged over all windows of size L that contain the base  pair.  For  a
       sequence  of  length  n and a window size of L the algorithm uses only O(n+L*L) memory and
       O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short stable  RNA
       structures.

       Output  consists  of  a dot plot in postscript file, where the averaged pair probabilities
       can easily be parsed and visually inspected.

       The -u option makes i possible to compute the probability that a stretch of x  consequtive
       nucleotides is unpaired, which is useful for predicting possible binding sites. Again this
       probability is averaged over all windows containing the region.

       WARNING! Output format changed!!

       The output is a plain text matrix containing on each line a position  i  followed  by  the
       probability that i is unpaired, [i-1..i] is unpaired [i-2..i] is unpaired and so on to the
       probability that [i-x+1..i] is unpaired.

       -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:
              Command line options which alter the general behavior of this program

       -v, --verbose
              Be verbose.  (default=off)

       -W, --winsize=size
              Average the pair probabilities over windows of given size.  (default=`70')

       -L, --span=size
              Set the maximum allowed separation of a base pair to span.

              By setting the maximum base pair span no pairs  (i,j)  with  j-i  >  span  will  be
              allowed. Defaults to winsize if parameter is omitted.

       -c, --cutoff=FLOAT
              Report  only  base  pairs  with  an  average  probability > cutoff in the dot plot.
              (default=`0.01')

       -o, --print_onthefly
              Save memory by printing out everything during computation.  (default=off)

              NOTE: activated per default for sequences over 1M bp.

       -u, --ulength=length
              Compute the mean probability that regions  of  length  1  to  a  given  length  are
              unpaired.  (default=`31')

              Output is saved in a _lunp file.

       -O, --opening_energies
              Switch output from probabilities to their logarithms.  (default=off)

              This  is  NOT  exactly the mean energies needed to unfold the respective stretch of
              bases! (implies --ulength option).

       --plex_output
              Create additional output files for RNAplex.  (default=off)

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

       --auto-id
              Automatically generate an ID for each sequence.  (default=off)

              The default mode of RNAplfold is to automatically determine an ID  from  the  input
              sequence  data if the input file format allows to do that. Sequence IDs are usually
              given in the FASTA header of input sequences. If this  flag  is  active,  RNAplfold
              ignores any IDs retrieved from the input and automatically generates an ID for each
              sequence. This ID consists of a prefix and an increasing number. This flag can also
              be used to add a FASTA header to the output even if the input has none.

       --id-prefix=prefix
              Prefix   for   automatically   generated  IDs  (as  used  in  output  file  names).
              (default=`sequence')

              If this parameter is set, each sequences'  FASTA  id  will  be  prefixed  with  the
              provided  string.  FASTA  ids  then  take the form ">prefix_xxxx" where xxxx is the
              sequence number. Hence, the output files will obey  the  following  naming  scheme:
              "prefix_xxxx_dp.ps"  (dot-plot),  "prefix_xxxx_lunp" (unpaired probabilities), etc.
              Note: Setting this parameter implies --auto-id.

       --id-delim=STRING
              Change the  delimiter  between  prefix  and  increasing  number  for  automatically
              generated IDs (as used in output file names).  (default=`_')

              This parameter can be used to change the default delimiter "_" between

              the prefix string and the increasing number for automatically generated ID.

       --id-digits=INT
              Specify  the  number  of digits of the counter in automatically generated alignment
              IDs.  (default=`4')

              When alignments IDs are automatically generated, they receive an increasing number,
              starting with 1. This number will always be left-padded by leading zeros, such that
              the number takes up a certain  width.  Using  this  parameter,  the  width  can  be
              specified  to  the  users  need.  We allow numbers in the range [1:18]. This option
              implies --auto-id.

       --id-start=LONG
              Specify the first number in automatically generated alignment IDs.  (default=`1')

              When sequence IDs are automatically generated, they receive an  increasing  number,
              usually starting with 1. Using this parameter, the first number can be specified to
              the users requirements. Note: negative numbers are not allowed.  Note: Setting this
              parameter  implies  to  ignore  any  IDs  retrieved  from  the  input data, i.e. it
              activates the --auto-id flag.

       --filename-delim=STRING
              Change  the  delimiting  character  that   is   used   for   sanitized   filenames.
              (default=`ID-delimiter')

              This parameter can be used to change the delimiting character used while sanitizing
              filenames, i.e. replacing invalid characters.  Note,  that  the  default  delimiter
              ALWAYS  is  the  first  character  of  the  "ID  delimiter" as supplied through the
              --id-delim option. If the delimiter is a whitespace  character  or  empty,  invalid
              characters will be simply removed rather than substituted. Currently, we regard the
              following characters as illegal for use in filenames:  backslash  '\',  slash  '/',
              question  mark  '?',  percent  sign  '%', asterisk '*', colon ':', pipe symbol '|',
              double quote '"', triangular brackets '<' and '>'.

       --filename-full
              Use full FASTA header to create filenames.  (default=off)

              This parameter can be used to deactivate the default behavior  of  limiting  output
              filenames  to the first word of the sequence ID. Consider the following example: An
              input with FASTA header ">NM_0001 Homo Sapiens some gene" usually  produces  output
              files  with the prefix "NM_0001" without the additional data available in the FASTA
              header, e.g. "NM_0001_dp.ps". With this flag  set,  no  truncation  of  the  output
              filenames  is  performed, i.e.  output filenames receive the full FASTA header data
              as prefixes. Note, however, that invalid characters (such as  whitespace)  will  be
              substituted  by  a  delimiting character or simply removed, (see also the parameter
              option --filename-delim).

       --shape=<filename>
              Use SHAPE reactivity data to guide structure predictions.

       --shapeMethod=STRING
              Specify  the  method  how  to  convert  SHAPE  reactivity  data  to  pseudo  energy
              contributions.  (default=`D')

              The  following methods can be used to convert SHAPE reactivities into pseudo energy
              contributions.

              'D': Convert by using a linear  equation  according  to  Deigan  et  al  2009.  The
              calculated  pseudo  energies  will  be  applied  for every nucleotide involved in a
              stacked pair. This method is recognized by a capital 'D' in the provided parameter,
              i.e.: --shapeMethod="D" is the default setting. The slope 'm' and the intercept 'b'
              can be set to a non-default value if necessary,  otherwise  m=1.8  and  b=-0.6.  To
              alter  these  parameters,  e.g. m=1.9 and b=-0.7, use a parameter string like this:
              --shapeMethod="Dm1.9b-0.7". You may also provide only one  of  the  two  parameters
              like: --shapeMethod="Dm1.9" or --shapeMethod="Db-0.7".

              'Z':  Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al
              2012. SHAPE reactivities will be converted to pairing probabilities by using linear
              mapping.  Aberration  from  the  observed  pairing  probabilities will be penalized
              during the folding recursion. The  magnitude  of  the  penalties  can  affected  by
              adjusting the factor beta (e.g. --shapeMethod="Zb0.8").

              'W':  Apply  a  given  vector  of  perturbation  energies  to  unpaired nucleotides
              according to Washietl et al 2012. Perturbation vectors can be calculated  by  using
              RNApvmin.

       --shapeConversion=STRING
              Specify the method used to convert SHAPE reactivities to pairing probabilities when
              using the SHAPE approach of Zarringhalam et al.  (default=`O')

              The  following  methods  can  be  used  to  convert  SHAPE  reactivities  into  the
              probability for a certain nucleotide to be unpaired.

              'M': Use linear mapping according to Zarringhalam et al.

              'C':  Use  a  cutoff-approach  to divide into paired and unpaired nucleotides (e.g.
              "C0.25")

              'S':  Skip  the  normalizing  step  since  the  input   data   already   represents
              probabilities for being unpaired rather than raw reactivity values

              'L':  Use  a  linear  model  to convert the reactivity into a probability for being
              unpaired (e.g. "Ls0.68i0.2" to use a slope of 0.68 and an intercept of 0.2)

              'O': Use a linear model to convert the log of the reactivity into a probability for
              being unpaired (e.g. "Os1.6i-2.29" to use a slope of 1.6 and an intercept of -2.29)

       --commands=<filename>
              Read additional commands from file.

              Commands  include  hard  and soft constraints, but also structure motifs in hairpin
              and interior loops that need to be treeted differently. Furthermore,  commands  can
              be set for unstructured and structured domains.

   Model Details:
       -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  while  -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.

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

              In  the  calculation of the partition function use pfScale * average_free_energy 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 longer folding
              windows.

       -b, --binaries
              Output accessibility profiles in binary format.  (default=off)

              The binary files produced by RNAplfold do not need to be parsed by RNAplex,

              so that they are directly loaded into memory. This is useful when  large  sequences
              have  to  be  searched  for  putative hybridization sites. Another advantage of the
              binary format is the 50% file size decrease.

       --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.

       --betaScale=DOUBLE
              Set the scaling of the Boltzmann factors.  (default=`1.')

              The  argument  provided  with  this  option  enables  to  scale  the  thermodynamic
              temperature  used  in the Boltzmann factors independently from the temperature used
              to scale the individual energy contributions  of  the  loop  types.  The  Boltzmann
              factors  then  become exp(-dG/(kT*betaScale)) where k is the Boltzmann constant, dG
              the free energy contribution of the state and T the absolute temperature.

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

       S. H. Bernhart, U. Mueckstein, and I.L.  Hofacker  (2011),  "RNA  Accessibility  in  cubic
       time", Algorithms Mol Biol. 6: 3.

       S.  H. Bernhart, I.L. Hofacker, and P.F. Stadler (2006), "Local Base Pairing Probabilities
       in Large RNAs", Bioinformatics: 22, pp 614-615

       A.F. Bompfuenewerer, R. Backofen, S.H. Bernhart, J. Hertel, I.L. Hofacker,  P.F.  Stadler,
       S. Will (2007), "Variations on RNA Folding and Alignment: Lessons from Benasque", J. Math.
       Biol.

       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

       Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler, 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.

SEE ALSO

       RNALfold(1)