Ubuntu Manpage: RNALfold - manual page for RNALfold 2.7.0

Provided by: vienna-rna_2.7.0+dfsg-1_amd64

NAME

       RNALfold - manual page for RNALfold 2.7.0

SYNOPSIS

       RNALfold [OPTION]...

DESCRIPTION

RNALfold 2.7.0

calculate locally stable secondary structures of RNAs

Compute locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n
and a base pair span 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 RNA structures. Output consists of a list of secondary
structure components of size <= L, one entry per line. Each output line contains the predicted local
structure its energy in kcal/mol and the starting position of the local structure.

-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

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

Lower the log level setting such that even INFO messages are passed through.

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 RNALfold is to read input from stdin. Using this parameter the user can
specify an input file name where data is read from.

-o, --outfile[=filename]
Print output to file instead of stdout.

This option may be used to write all output to output files rather than printing to stdout. The
number of output files created for batch input (multiple sequences) depends on three conditions:
(i) In case an optional filename is given as parameter argument, a single file with the specified
filename will be written into. If the optional argument is omitted, (ii) FASTA input or an active
--auto-id switch will write to multiple files that follow the naming scheme "prefix.lfold". Here,
"prefix" is taken from the sequence id as specified in the FASTA header. Lastly, (iii) single-line
sequence input without FASTA header will be written to a single file "RNALfold_output.lfold". In
case an output file already exists, any output of the program will be appended to it. Since the
filename argument is optional, it must immediately follow the short option flag to not be mistaken
as new parameter to the program. For instance \'-ornafold.out\' will write to a file
"rnafold.out". Note: Any special characters in the filename will be replaced by the filename
delimiter, hence there is no way to pass an entire directory path through this option yet. (See
also the "--filename-delim" parameter)

--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 RNALfold 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, RNALfold 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 sequence will be prefixed with the provided string. Hence, the
output files will obey the following naming scheme: "prefix_xxxx.lfold" 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 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=CHAR
Change the delimiting character used in 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_ss.ps" for secondary structure
plots. With this flag set, no truncation of the output filenames is done, 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).

--log-level=level
Set log level threshold. (default=`2')

By default, any log messages are filtered such that only warnings (level 2) or errors (level 3)
are printed. This setting allows for specifying the log level threshold, where higher values
result in fewer information. Log-level 5 turns off all messages, even errors and other critical
information.

--log-file[=filename]
Print log messages to a file instead of stderr. (default=`RNALfold.log')

--log-time
Include time stamp in log messages.

(default=off)

--log-call
Include file and line of log calling function.

(default=off)

Algorithms:
Select additional algorithms which should be included in the calculations. The Minimum free
energy (MFE) and a structure representative are calculated in any case.

-L, --span=INT
Set the maximum distance between any two pairing nucleotides.

(default=`150')

This option specifies the window length L and therefore the upper limit for the distance between
the bases i and j of any pair (i, j), i.e. (j - i + 1) <= L.

-z, --zscore[=DOUBLE]
Limit the output to predictions with a Z-score below a threshold.

(default=`-2')

This option activates z-score regression using a trained SVM. Any predicted structure that exceeds
the specified threshold will be ommited from the output. Since the Z-score threshold is given as
a negative number, it must immediately preceed the short option to not be mistaken as a separate
argument, e.g. -z-2.9 sets the threshold to a value of -2.9

--zscore-pre-filter
Apply the z-score filtering in the forward recursions.

(default=off)

The default mode of z-score filtering considers the entire structure space to decide whether or
not a locally optimal structure at any position i is reported or not. When using this
post-filtering step, however, alternative locally optimal structures

starting at i with higher energy but lower z-score can be easily missed. The

pre-filter

option restricts the structure space already in the forward recursions, such

that

only optimal solution among those candidates that satisfy the z-score

threshold are considered. Therefore, good results according to the z-score threshold criterion are
less likely to be superseded by results with better energy but worse z-score. Note, that
activating this switch results in higher computation time which scales linear in the window
length.

--zscore-report-subsumed
Report subsumed structures if their z-score is less than that of the enclosing structure.

(default=off)

In default mode, RNALfold only reports locally optimal structures if they are no constituents of
another, larger structure with less free energy. In z-score mode, however, such a larger structure
may have a higher z-score, thus may be less informative than the smaller substructure. Using this
switch activates reporting both, the smaller and the larger structure if the z-score of the
smaller is lower than that of the larger.

-b, --backtrack-global
Backtrack a global MFE structure. (default=off)

Instead of just reporting the locally stable secondary structure a global MFE structure can be
constructed that only consists of locally optimal substructures. This switch activates a
post-processing step that takes the locally optimal structures to generate the global MFE
structure which constitutes the MFE value reported in the last line. The respective global MFE
structure is printed just after the inut sequence part on the last line, preceding the global MFE
score. Note, that this option implies -o/--outfile since the locally optimal structures must be
read after the regular prediction step! Also note, that using this option in combination with
-z/--zscore implies --zscore-pre-filter to ensure proper construction of the global MFE structure!

-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

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

--shapeMethod=method
Select SHAPE reactivity data incorporation strategy.

(default=`D')

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

'D': Convert by using the linear equation according to Deigan et al 2009.

Derived pseudo energy terms 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=method
Select method for SHAPE reactivity conversion.

(default=`O')

This parameter is useful when dealing with the SHAPE incorporation according to Zarringhalam et
al. 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 internal
loops that need to be treeted differently. Furthermore, commands can be set for unstructured and
structured domains.

Energy Parameters:
Energy parameter sets can be adapted or loaded from user-provided input files

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

(default=`37.0')

-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.

-m, --modifications[=STRING]
Allow for modified bases within the RNA sequence string.

(default=`7I6P9D')

Treat modified bases within the RNA sequence differently, i.e. use corresponding energy
corrections and/or pairing partner rules if available. For that, the modified bases in the input
sequence must be marked by their corresponding one-letter code. If no additional arguments are
supplied, all available corrections are performed. Otherwise, the user may limit the modifications
to a particular subset of modifications, resp. one-letter codes, e.g. -mP6 will only correct for
pseudouridine and m6A bases.

Currently supported one-letter codes and energy corrections are:

'7': 7-deaza-adenonsine (7DA)

'I': Inosine

'6': N6-methyladenosine (m6A)

'P': Pseudouridine

'9': Purine (a.k.a. nebularine)

'D': Dihydrouridine

--mod-file=STRING
Use additional modified base data from JSON file.

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 -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 (-p). 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 enclosed pairs in a loop of degree 3 and works only for mfe folding.

Note that with -d1 and -d3 only the MFE computations will be using this setting while partition
function uses -d2 setting, i.e. dangling ends will be treated differently.

--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.

--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 (--energyModel 1) or AU (--energyModel 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

       I.L. Hofacker, B. Priwitzer, and P.F.  Stadler  (2004),  "Prediction  of  Locally  Stable  RNA  Secondary
       Structures for Genome-Wide Surveys", Bioinformatics: 20, pp 186-190

       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.

NAME

SYNOPSIS

DESCRIPTION

REFERENCES

AUTHOR

REPORTING BUGS

SEE ALSO