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RNAPLFOLD(1)			 User Commands			  RNAPLFOLD(1)

NAME
       RNAplfold - manual page for RNAplfold 2.4.14

SYNOPSIS
       RNAplfold [OPTIONS]...

DESCRIPTION
       RNAplfold 2.4.14

       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  con-
       tain  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	struc-
       tures.

       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.  I.e.
	      no pairs (i,j) with j-i >	span will be allowed. Defaults to win-
	      size 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.
	      NOTE: activated per default for sequences	over 1M	bp.

	      (default=off)

       -u, --ulength=length
	      Compute the mean probability that	regions	of length 1 to a given
	      length are unpaired.  Output is saved in a _lunp file.

	      (default=`31')

       -O, --opening_energies
	      Switch  output from probabilities	to their logarithms, which are
	      NOT exactly the mean energies needed to the  respective  stretch
	      of bases!	 NOTE: This actives -u option.

	      (default=off)

       --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  in-
	      creasing	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 pre-
	      fixed 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:	 "pre-
	      fix_xxxx_dp.ps"  (dot-plot), "prefix_xxxx_lunp" (unpaired	proba-
	      bilities), etc. Note: Setting this parameter implies --auto-id.

       --id-delim=delimiter
	      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 parame-
	      ter, the first number can	be specified  to  the  users  require-
	      ments.  Note:  negative  numbers are not allowed.	 Note: Setting
	      this parameter implies to	ignore any IDs retrieved from the  in-
	      put data,	i.e. it	activates the --auto-id	flag.

       --filename-delim=delimiter
	      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  charac-
	      ters. Note, that the default delimiter ALWAYS is the first char-
	      acter of the "ID delimiter" as supplied through  the  --id-delim
	      option. If the delimiter is a whitespace character or empty, in-
	      valid characters will be simply removed rather than substituted.
	      Currently, we regard the following characters as illegal for use
	      in filenames: backslash '\', slash '/', question mark '?',  per-
	      cent  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=[D/Z/W] + [optional parameters]
	      Select method to incorporate SHAPE reactivity

       data.  (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  ev-
	      ery nucleotide involved in a stacked pair. This method is	recog-
	      nized  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 vec-
	      tors can be calculated by	using RNApvmin.

       --shapeConversion=M/C/S/L/O
	      +	[optional parameters] Select method to convert SHAPE reactivi-
	      ties to

       pairing probabilities.
	      (default=`O')

	      This  parameter is useful	when dealing with the SHAPE incorpora-
	      tion according to	Zarringhalam et	al. 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 nucleo-
	      tides (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 reactiv-
	      ity 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 of temp C. Default is
	      37C.

       -4, --noTetra
	      Do  not include special tabulated	stabilizing energies for tri-,
	      tetra- and hexaloop hairpins. Mostly for testing.

	      (default=off)

       -d, --dangles=INT
	      How to treat "dangling end" energies for bases adjacent  to  he-
	      lices 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.

       -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 oc-
	      cur 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  de-
	      fault parameter set.

	      Different	 sets  of energy parameters for	RNA and	DNA should ac-
	      company your distribution.  See the RNAlib documentation for de-
	      tails 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=scaling factor
	      In the calculation of the	partition function use pfScale * aver-
	      age_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 hybridiza-
	      tion  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
	      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 indepen-
	      dently  from the temperature used	to scale the individual	energy
	      contributions of the loop	types. The Boltzmann factors then  be-
	      come  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	Struc-
       tures", 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  Accessi-
       bility 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.  Ho-
       facker,	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 modifica-
       tion 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)

RNAplfold 2.4.14		  August 2019			  RNAPLFOLD(1)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS | SEE ALSO

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