RNAEVAL(1)

NAME
RNAeval - manual page for RNAeval 2.4.3

SYNOPSIS
RNAeval [OPTIONS]...

DESCRIPTION
RNAeval 2.4.3

calculate energy of RNA sequences with given secondary structure

Evaluates the free energy of an RNA molecule in fixed secondary structure. Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written to stdout. The program will continue to read new sequences and structures until a line consisting of the single character "@" or an end of file condition is encountered. If the input sequence or structure contains the separator character "&" the program calculates the energy of the co-folding of two RNA strands, where the "&" marks the boundary between the two strands.

-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

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

    (default=off)

-v, --verbose
    Print out energy contribution of each loop in the structure.

    (default=off)

--auto-id
    Automatically generate an ID for each sequence. (default=off)

    The default mode of RNAeval 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, RNAeval 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 sequence will be prefixed with the provided string. 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:

-T, --temp=DOUBLE
    Rescale energy parameters to a temperature of temp C. Default is 37C.

-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 -d1 only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the default for mfe and partition function folding. The option -d0 ignores dangling ends altogether (mostly for debugging). With -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3.

-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.

-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. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.

-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)

--logML
    Recalculate energies of structures using a logarithmic energy function for multi-loops before output.

    (default=off)

    This option does not effect structure generation, only the energies that are printed out. Since logML lowers energies somewhat, some structures may be missing.

--shape=SHAPE file
    Use SHAPE reactivity data in the folding recursions (does not work for PF yet)

--shapeMethod=[D/Z/W] + [optional parameters]
    Specify the method how to convert SHAPE

reactivity data to pseudo energy
    contributions

    (default=`D')

    The following methods can be used to convert SHAPE reactivities into pseudo energy contributions.

    'D': Convert by using a linear equation according to Deigan et al 2009. The calculated pseudo energies will be applied for every nucleotide involved in a stacked pair. This method is recognized by a capital 'D' in the provided parameter, i.e.: --shapeMethod="D" is the default setting. The slope 'm' and the intercept 'b' can be set to a non-default value if necessary, otherwise m=1.8 and b=-0.6. To alter these parameters, e.g. m=1.9 and b=-0.7, use a parameter string like this: --shapeMethod="Dm1.9b-0.7". You may also provide only one of the two parameters like: --shapeMethod="Dm1.9" or --shapeMethod="Db-0.7".

    'Z': Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012. SHAPE reactivities will be converted to pairing probabilities by using linear mapping. Aberration from the observed pairing probabilities will be penalized during the folding recursion. The magnitude of the penalties can affected by adjusting the factor beta (e.g. --shapeMethod="Zb0.8").

    'W': Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012. Perturbation vectors can be calculated by using RNApvmin.

--shapeConversion=M/C/S/L/O
    + [optional parameters] Specify the method used to convert SHAPE

reactivities to pairing probabilities when
    using the SHAPE approach of Zarringhalam et al.

    (default=`O')

    The following methods can be used to convert SHAPE reactivities into the probability for a certain nucleotide to be unpaired.

    'M': Use linear mapping according to Zarringhalam et al. 'C': Use a cutoff-approach to divide into paired and unpaired nucleotides (e.g. "C0.25") 'S': Skip the normalizing step since the input data already represents probabilities for being unpaired rather than raw reactivity values 'L': Use a linear model to convert the reactivity into a probability for being unpaired (e.g. "Ls0.68i0.2" to use a slope of 0.68 and an intercept of 0.2) 'O': Use a linear model to convert the log of the reactivity into a probability for being unpaired (e.g. "Os1.6i-2.29" to use a slope of 1.6 and an intercept of -2.29)

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 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.