Ubuntu Manpage: RNAplfold - manual page for RNAplfold 2.4.17

Provided by: vienna-rna_2.4.17+dfsg-2build2_amd64

NAME

       RNAplfold - manual page for RNAplfold 2.4.17

SYNOPSIS

       RNAplfold [OPTION]...

DESCRIPTION

RNAplfold 2.4.17

calculate locally stable secondary structure - pair probabilities

Computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged
over all windows of size L that contain the base pair. For a sequence of length n and a window size of L
the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large
genomes for short stable RNA structures.

Output consists of a dot plot in postscript file, where the averaged pair probabilities can easily be
parsed and visually inspected.

The -u option makes i possible to compute the probability that a stretch of x consequtive nucleotides is
unpaired, which is useful for predicting possible binding sites. Again this probability is averaged over
all windows containing the region.

WARNING! Output format changed!!

The output is a plain text matrix containing on each line a position i followed by the probability that i
is unpaired, [i-1..i] is unpaired [i-2..i] is unpaired and so on to the probability that [i-x+1..i] is
unpaired.

-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:
Command line options which alter the general behavior of this program

-v, --verbose
Be verbose. (default=off)

-W, --winsize=size
Average the pair probabilities over windows of given size. (default=`70')

-L, --span=size
Set the maximum allowed separation of a base pair to span.

By setting the maximum base pair span no pairs (i,j) with j-i > span will be allowed. Defaults to
winsize if parameter is omitted.

-c, --cutoff=FLOAT
Report only base pairs with an average probability > cutoff in the dot plot. (default=`0.01')

-o, --print_onthefly
Save memory by printing out everything during computation. (default=off)

NOTE: activated per default for sequences over 1M bp.

-u, --ulength=length
Compute the mean probability that regions of length 1 to a given length are unpaired.
(default=`31')

Output is saved in a _lunp file.

-O, --opening_energies
Switch output from probabilities to their logarithms. (default=off)

This is NOT exactly the mean energies needed to unfold the respective stretch of bases! (implies
--ulength option).

--plex_output
Create additional output files for RNAplex. (default=off)

--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 RNAplfold 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, RNAplfold 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. Hence, the output
files will obey the following naming scheme: "prefix_xxxx_dp.ps" (dot-plot), "prefix_xxxx_lunp"
(unpaired probabilities), etc. Note: Setting this parameter implies --auto-id.

--id-delim=STRING
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.

--filename-delim=STRING
Change the delimiting character that is used for sanitized filenames. (default=`ID-delimiter')

This parameter can be used to change the delimiting character used while sanitizing filenames,
i.e. replacing invalid characters. Note, that the default delimiter ALWAYS is the first character
of the "ID delimiter" as supplied through the --id-delim option. If the delimiter is a whitespace
character or empty, invalid characters will be simply removed rather than substituted. Currently,
we regard the following characters as illegal for use in filenames: backslash '\', slash '/',
question mark '?', percent sign '%', asterisk '*', colon ':', pipe symbol '|', double quote '"',
triangular brackets '<' and '>'.

--filename-full
Use full FASTA header to create filenames. (default=off)

This parameter can be used to deactivate the default behavior of limiting output filenames to the
first word of the sequence ID. Consider the following example: An input with FASTA header
">NM_0001 Homo Sapiens some gene" usually produces output files with the prefix "NM_0001" without
the additional data available in the FASTA header, e.g. "NM_0001_dp.ps". With this flag set, no
truncation of the output filenames is performed, i.e. output filenames receive the full FASTA
header data as prefixes. Note, however, that invalid characters (such as whitespace) will be
substituted by a delimiting character or simply removed, (see also the parameter option
--filename-delim).

--shape=<filename>
Use SHAPE reactivity data to guide structure predictions.

--shapeMethod=STRING
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=STRING
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)

--commands=<filename>
Read additional commands from file.

Commands include hard and soft constraints, but also structure motifs in hairpin and interior
loops that need to be treeted differently. Furthermore, commands can be set for unstructured and
structured domains.

Model Details:
-T, --temp=DOUBLE
Rescale energy parameters to a temperature in degrees centigrade. (default=`37.0')

-4, --noTetra
Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins.
(default=off)

Mostly for testing.

-d, --dangles=INT
Specify "dangling end" model 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 while -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.

-S, --pfScale=DOUBLE
Set scaling factor for Boltzmann factors to prevent under/overflows.

In the calculation of the partition function use pfScale * average_free_energy as an estimate for
the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to
1.2. Occasionally needed for longer folding windows.

-b, --binaries
Output accessibility profiles in binary format. (default=off)

The binary files produced by RNAplfold do not need to be parsed by RNAplex,

so that they are directly loaded into memory. This is useful when large sequences have to be
searched for putative hybridization sites. Another advantage of the binary format is the 50% file
size decrease.

--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.

-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.

--betaScale=DOUBLE
Set the scaling of the Boltzmann factors. (default=`1.')

The argument provided with this option enables to scale the thermodynamic temperature used in the
Boltzmann factors independently from the temperature used to scale the individual energy
contributions of the loop types. The Boltzmann factors then become exp(-dG/(kT*betaScale)) where k
is the Boltzmann constant, dG the free energy contribution of the state and T the absolute
temperature.

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

       S. H. Bernhart, U. Mueckstein, and I.L. Hofacker (2011), "RNA Accessibility in  cubic  time",  Algorithms
       Mol Biol. 6: 3.

       S. H. Bernhart, I.L. Hofacker, and P.F. Stadler (2006), "Local Base Pairing Probabilities in Large RNAs",
       Bioinformatics: 22, pp 614-615

       A.F. Bompfuenewerer, R. Backofen, S.H. Bernhart, J. Hertel, I.L. Hofacker, P.F. Stadler, S. Will  (2007),
       "Variations on RNA Folding and Alignment: Lessons from Benasque", J. Math. Biol.

       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

       Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler, Ronny Lorenz

REPORTING BUGS