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RNALFOLD(1)			 User Commands			   RNALFOLD(1)

NAME
       RNALfold	- manual page for RNALfold 2.4.14

SYNOPSIS
       RNALfold	[OPTIONS]...

DESCRIPTION
       RNALfold	2.4.14

       calculate locally stable	secondary structures of	RNAs

       Compute locally stable RNA secondary structure with a maximal base pair
       span.  For a sequence of	length n and a base pair span of L  the	 algo-
       rithm uses only O(n+L*L)	memory and O(n*L*L) CPU	time. Thus it is prac-
       tical to	"scan" very large genomes for short  RNA  structures.	Output
       consists	 of a list of secondary	structure components of	size <=	L, one
       entry per line. Each output line	contains the predicted local structure
       its  energy  in	kcal/mol and the starting position of the local	struc-
       ture.

       -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

       -v, --verbose
	      Be verbose

	      (default=off)

       -L, --span=INT
	      Set the maximum distance between any two pairing nucleotides.

	      (default=`150')

	      This  option specifies the window	length L and therefore the up-
	      per limit	for the	distance between the bases i and j of any pair
	      (i, j), i.e. (j -	i + 1) <= L.

       --noconv
	      Do not automatically substitude nucleotide "T" with "U"

	      (default=off)

       -o, --outfile[=<filename>]
	      Print output to file instead of stdout

	      This  option  may	 be  used  to write all	output to output files
	      rather than printing to stdout. The number of output files  cre-
	      ated  for	batch input (multiple sequences) depends on three con-
	      ditions: (i) In case an optional filename	is given as  parameter
	      argument,	 a  single  file  with	the specified filename will be
	      written into. If the optional argument is	 omitted,  (ii)	 FASTA
	      input or an active --auto-id switch will write to	multiple files
	      that follow the naming scheme "prefix.lfold". Here, "prefix"  is
	      taken  from  the	sequence  id as	specified in the FASTA header.
	      Lastly, (iii) single-line	sequence input	without	 FASTA	header
	      will  be	written	 to  a single file "RNALfold_output.lfold". In
	      case an output file already exists, any output  of  the  program
	      will  be	appended  to  it.   Since the filename argument	is op-
	      tional, it must immediately follow the short option flag to  not
	      be mistaken as new parameter to the program. For instance	\'-or-
	      nafold.out\' will	write to a file	"rnafold.out".	Note: Any spe-
	      cial characters in the filename will be replaced by the filename
	      delimiter, hence there is	no way to  pass	 an  entire  directory
	      path  through  this option yet. (See also	the "--filename-delim"
	      parameter)

       -i, --infile=<filename>
	      Read a file instead of reading from stdin

	      The default behavior of RNALfold is to read  input  from	stdin.
	      Using  this  parameter  the  user	can specify an input file name
	      where data is read from.

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

	      The default mode of RNALfold 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, RNALfold ignores any
	      IDs retrieved from the input and automatically generates	an  ID
	      for  each	sequence. This ID consists of a	prefix and an increas-
	      ing number. This flag can	also be	used to	add a FASTA header  to
	      the output even if the input has none.

       --id-prefix=prefix
	      Set prefix for automatically generated IDs (default=`sequence')

	      If  this	parameter  is set, each	sequence will be prefixed with
	      the provided string. Hence, the output files will	obey the  fol-
	      lowing  naming scheme: "prefix_xxxx.lfold" where xxxx is the se-
	      quence number. Note: Setting this	parameter implies --auto-id.

       --id-delim=delimiter
	      Change prefix delimiter for automatically	generated ids.

	      (default=`_')

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

	      the  prefix  string  and the increasing number for automatically
	      generated	IDs

       --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.lfold". 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).

       --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.

   Algorithms:
	      Select additional	algorithms which should	 be  included  in  the
	      calculations.   The  Minimum  free  energy (MFE) and a structure
	      representative are calculated in any case.

       -z, --zscore[=DOUBLE]
	      Limit the	output to predictions with a Z-score below a threshold

	      (default=`-2')

	      This option activates z-score regression using  a	 trained  SVM.
	      Any  predicted  structure	 that  exceeds the specified threshold
	      will be ommited from the output.	Since the Z-score threshold is
	      given  as	 a  negative  number,  it must immediately preceed the
	      short option to not be mistaken as  a  separate  argument,  e.g.
	      -z-2.9 sets the threshold	to a value of -2.9

       -g, --gquad
	      Incoorporate  G-Quadruplex  formation into the structure predic-
	      tion algorithm

	      (default=off)

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

       --shapeMethod=D/Z/W
	      Include SHAPE reactivity data according to a particular method.

	      (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=type
	      Convert SHAPE reactivity according to a particular model.

	      (default=`O')

	      This method allows one to	specify	the method or  model  used  to
	      convert  SHAPE  reactivities to pairing (or unpaired) probabili-
	      ties when	using the SHAPE	approach of Zarringhalam et al.	 2012.
	      The following single letter types	are recognized:

	      'M': Use linear mapping according	to Zarringhalam	et al. 2012.

	      '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 rep-
	      resents  probabilities  for being	unpaired rather	than raw reac-
	      tivity values

	      'L': Use a linear	model to convert the reactivity	into a	proba-
	      bility  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)

   Model Details:
	      You may tweak the	energy model and  pairing  rules  additionally
	      using the	following parameters

       -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.

	      (default=off)

       -d, --dangles=INT
	      Change the dangling end model (default=`2')

	      This option allows one to	change the model "dangling end"	energy
	      contributions, i.e. those	additional  contributions  from	 bases
	      adjacent	to  helices in free ends and multi-loops With -d1 only
	      unpaired bases can participate in	 at  most  one	dangling  end.
	      With  -d2	this check is ignored, dangling	energies will be added
	      for the bases adjacent to	a helix	on both	 sides	in  any	 case;
	      this is the default for mfe and partition	function folding (-p).
	      The option -d0 ignores dangling ends altogether (mostly  for de-
	      bugging).	  With	-d3 mfe	folding	will allow coaxial stacking of
	      adjacent helices in multi-loops. At the moment  the  implementa-
	      tion  will  not allow coaxial stacking of	the two	interior pairs
	      in a loop	of degree 3 and	works only for mfe folding.

	      Note that	with -d1 and -d3 only the MFE computations will	be us-
	      ing this setting while partition function	uses -d2 setting, i.e.
	      dangling ends will be treated differently.

       --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.

       --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. RNALfold -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.

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

       I.L.  Hofacker,	B.  Priwitzer, and P.F.	Stadler	(2004),	"Prediction of
       Locally Stable  RNA  Secondary  Structures  for	Genome-Wide  Surveys",
       Bioinformatics: 20, pp 186-190

       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
       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
       RNAplfold(1) RNALalifold(1)

RNALfold 2.4.14			  August 2019			   RNALFOLD(1)

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

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