Provided by: vienna-rna_2.6.4+dfsg-1build1_amd64 
NAME
RNAheat - manual page for RNAheat 2.6.4
SYNOPSIS
RNAheat [OPTIONS] [<input0>] [<input1>]...
DESCRIPTION
RNAheat 2.6.4
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
I/O Options:
Command line options for input and output (pre-)processing
-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.
-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.
--noconv
Do not automatically substitute nucleotide "T" with "U".
(default=off)
--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=STRING
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=CHAR
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.
Algorithms:
Select additional algorithms which should be included in the calculations.
--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')
-c, --circ
Assume a circular (instead of linear) RNA molecule.
(default=off)
-g, --gquad
Incoorporate G-Quadruplex formation into the structure prediction algorithm.
(default=off)
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')
Energy Parameters:
Energy parameter sets can be adapted or loaded from user-provided input files
-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. The
placeholder file name 'DNA' can be used to load DNA parameters without the need to
actually specify any input file.
-4, --noTetra
Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop
hairpins.
(default=off)
Mostly for testing.
--salt=DOUBLE
Set salt concentration in molar (M). Default is 1.021M.
Model Details:
Tweak the energy model and pairing rules additionally using the following
parameters
-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)
--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.
--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.
--helical-rise=FLOAT
Set the helical rise of the helix in units of Angstrom.
(default=`2.8')
Use with caution! This value will be re-set automatically to 3.4 in case DNA
parameters are loaded via -P DNA and no further value is provided.
--backbone-length=FLOAT
Set the average backbone length for looped regions in units of Angstrom.
(default=`6.0')
Use with caution! This value will be re-set automatically to 6.76 in case DNA
parameters are loaded via -P DNA and no further value is provided.
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)