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RNAHEAT

NAME

RNAheat − manual page for RNAheat 2.4.11

SYNOPSIS

RNAheat [options]

DESCRIPTION

RNAheat 2.4.11

calculate specific heat of RNAs

Reads RNA sequences from stdin 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)

−−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.

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.

A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format.

−−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)

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)