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RNAHEAT(1)			 User Commands			    RNAHEAT(1)

       RNAheat - manual	page for RNAheat 2.4.14

       RNAheat [OPTIONS] [_input0_] [_input1_]...

       RNAheat 2.4.14

       calculate specific heat of RNAs

       Reads RNA sequences from	stdin or input files and calculates their spe-
       cific heat in the temperature range t1 to t2, from the partition	 func-
       tion  by	 numeric differentiation. The result is	written	to stdout as a
       list of pairs of	temperature in C and specific  heat  in	 Kcal/(Mol*K).
       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

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

	      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

	      Lowest temperature


	      Highest temperature


	      Calculate	partition function every stepsize degrees C


       -m, --ipoints=ipoints
	      The program fits a parabola to 2*ipoints+1 data points to	calcu-
	      late 2nd	derivatives.  Increasing  this	parameter  produces  a
	      smoother curve


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


       -j, --jobs[=number]
	      Split batch input	into jobs and start processing in parallel us-
	      ing multiple threads. A value of 0 indicates to use as many par-
	      allel threads as computation cores are available.


	      Default  processing of input data	is performed in	a serial fash-
	      ion, i.e.	one sequence at	a time.	Using this switch, a user  can
	      instead start the	computation for	many sequences in the input in
	      parallel.	RNAheat	will create as many parallel computation slots
	      as specified and assigns input sequences of the input file(s) to
	      the available slots. Note, that this increases  memory  consump-
	      tion  since  input alignments have to be kept in memory until an
	      empty compute slot is available and each	running	 job  requires
	      its own dynamic programming matrices.

	      Do  not  try  to	keep output in order with input	while parallel
	      processing is in place.


	      When parallel input processing (--jobs flag) is enabled, the or-
	      der in which input is processed depends on the host machines job
	      scheduler. Therefore, any	output to stdout or files generated by
	      this program will	most likely not	follow the order of the	corre-
	      sponding input data set. The default of RNAheat is to use	a spe-
	      cialized	data structure to still	keep the results output	in or-
	      der with the input data. However,	this comes with	a trade-off in
	      terms  of	 memory	 consumption, since all	output must be kept in
	      memory for as long as no chunks of consecutive,  ordered	output
	      are available. By	setting	this flag, RNAheat will	not buffer in-
	      dividual results but print them as soon as they have been	compu-

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

	      The  default  behavior of	RNAheat	is to read input from stdin or
	      the file(s) that follow(s) the RNAheat command. Using  this  pa-
	      rameter the user can specify input file names where data is read
	      from. Note, that any additional files supplied  to  RNAheat  are
	      still processed as well.

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

	      The  default mode	of RNAheat 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, RNAheat 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.

	      Prefix for automatically generated IDs (as used in  output  file


	      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. Note: Setting
	      this parameter implies --auto-id.

	      Change the delimiter between prefix and  increasing  number  for
	      automatically generated IDs (as used in output file names)


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

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

	      Specify  the  number  of	digits of the counter in automatically
	      generated	alignment IDs.


	      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.

	      Specify  the  first  number in automatically generated alignment


	      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.

   Structure Constraints:
	      Command  line options to interact	with the structure constraints
	      feature of this program

	      Set the maximum base pair	span


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


       -d, --dangles=INT
	      How  to  treat "dangling end" energies for bases adjacent	to he-
	      lices in free ends and multi-loops


	      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).

	      Produce structures without lonely	pairs (helices of length 1).


	      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


	      Do not allow GU pairs at the end of helices


       -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.

	      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. RNAheat -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.

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


       -c, --circ
	      Assume a circular	(instead of linear) RNA	molecule.


       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

       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

       Ivo L Hofacker, Peter F Stadler,	Ronny Lorenz

       If in doubt our program is right, nature	is at fault.  Comments	should
       be sent to


RNAheat	2.4.14			  August 2019			    RNAHEAT(1)


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