RNALfold - manual page for RNALfold 2.5.1
RNALfold [
OPTION]...
RNALfold 2.5.1
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
- Below are command line options which alter the general
behavior of this program
-
-v, --verbose
- Be verbose
- (default=off)
-
-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.
- --noconv
- Do not automatically substitude nucleotide "T"
with "U"
- (default=off)
-
-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)
-
-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.
- --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=prefix
- Set prefix for automatically generated IDs
(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=delimiter
- Change prefix delimiter for automatically generated
ids.
- (default=`_')
- This parameter can be used to change the default delimiter
"_" between
- the prefix string and the increasing number for
automatically generated IDs
-
--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=delimiter
- 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.lfold". 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).
-
--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.
- Select additional algorithms which should be included in
the calculations. The Minimum free energy (MFE) and a structure
representative are calculated in any case.
-
-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
this option in combination with -z/--zscore implies
--zscore-hard-filter to ensure proper construction of the global
MFE structure!
-
-g, --gquad
- Incoorporate G-Quadruplex formation into the structure
prediction algorithm
- (default=off)
-
--shape=<filename>
- Use SHAPE reactivity data to guide structure
predictions.
-
--shapeMethod=D/Z/W
- Include SHAPE reactivity data according to a particular
method.
- (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=type
- Convert SHAPE reactivity according to a particular
model.
- (default=`O')
- This method allows one to specify the method or model used
to convert SHAPE reactivities to pairing (or unpaired) probabilities when
using the SHAPE approach of Zarringhalam et al. 2012. The following single
letter types are recognized:
- 'M': Use linear mapping according to Zarringhalam et al.
2012.
- '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)
- You may tweak the energy model and pairing rules
additionally using the following parameters
-
-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.
- (default=off)
-
-d, --dangles=INT
- Change the dangling end model (default=`2')
- This option allows one to change the model "dangling
end" energy contributions, i.e. those additional contributions from
bases adjacent to helices in free ends and multi-loops 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 interior 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)
-
-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.
-
--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. RNALfold -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.
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
Ivo L Hofacker, Peter F Stadler, Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].
RNAplfold(1) RNALalifold(1)