RNAheat

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

.HP -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)