Provided by: vienna-rna_2.5.1+dfsg-1build3_amd64 
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)
RNAheat 2.5.1 April 2024 RNAHEAT(1)