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

NAME

       RNAheat - manual page for RNAheat 2.5.1

SYNOPSIS

       RNAheat [OPTIONS] [<input0>] [<input1>]...

DESCRIPTION

       RNAheat 2.5.1

       calculate specific heat of RNAs

       Reads  RNA  sequences  from stdin or input files and calculates their specific heat in the
       temperature range t1 to t2, from the partition function 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

       --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

       --Tmin=t1
              Lowest temperature

              (default=`0')

       --Tmax=t2
              Highest temperature

              (default=`100')

       --stepsize=FLOAT
              Calculate partition function every stepsize degrees C

              (default=`1.')

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

              (default=`2')

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

              (default=off)

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

              (default=`0')

              Default processing of input data  is  performed  in  a  serial  fashion,  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  consumption  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.

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

              (default=off)

              When  parallel  input processing (--jobs flag) is enabled, the order 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 corresponding input data set. The default of RNAheat is to  use  a  specialized
              data  structure  to  still  keep  the  results output in order 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  individual
              results but print them as soon as they have been computated.

       -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 parameter 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.

       --auto-id
              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.

       --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. 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 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.

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

       --maxBPspan=INT
              Set the maximum base pair span

              (default=`-1')

   Model Details:
       -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 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

       -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.
              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 prediction algorithm.

              (default=off)

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

              (default=off)

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

       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

       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

       RNAfold(1)