RNAcofold - manual page for RNAcofold 2.5.1
RNAcofold [
OPTION]... [
FILE]...
RNAcofold 2.5.1
calculate secondary structures of two RNAs with dimerization
The program works much like RNAfold, but allows one to specify two RNA sequences
which are then allowed to form a dimer structure. RNA sequences are read from
stdin in the usual format, i.e. each line of input corresponds to one
sequence, except for lines starting with ">" which contain the
name of the next sequence. To compute the hybrid structure of two molecules,
the two sequences must be concatenated using the \'&\' character as
separator. RNAcofold can compute minimum free energy (mfe) structures, as well
as partition function (pf) and base pairing probability matrix (using the
-p switch) Since dimer formation is concentration dependent, RNAcofold
can be used to compute equilibrium concentrations for all five monomer and
(homo/hetero)-dimer species, given input concentrations for the monomers.
Output consists of the mfe structure in bracket notation as well as PostScript
structure plots and "dot plot" files containing the pair
probabilities, see the RNAfold man page for details. In the dot plots a cross
marks the chain break between the two concatenated sequences. 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
- Command line options which alter the general behavior of
this program
-
-v, --verbose
- Be verbose.
- (default=off)
-
-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 pair at a time. Using this switch, a user can
instead start the computation for many sequence pairs in the input in
parallel. RNAcofold 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 RNAcofold 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, RNAcofold will not
buffer individual results but print them as soon as they have been
computated.
- --noPS
- Do not produce postscript drawing of the mfe
structure.
- (default=off)
- --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 RNAcofold 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, RNAcofold 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. Hence, the output files will obey the following
naming scheme: "prefix_xxxx_ss.ps" (secondary structure plot),
"prefix_xxxx_dp.ps" (dot-plot), "prefix_xxxx_dp2.ps"
(stack probabilities), etc. where xxxx is the sequence number. 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.
-
--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_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).
-
--output-format=format-character
- Change the default output format
- (default=`V')
- The following output formats are currently supported:
- ViennaRNA format (V), Delimiter-separated format (D) also
known as CSV
- format.
-
--csv-delim=delimiter
- Change the delimiting character for Delimiter-separated
output format, such as CSV
- (default=`,')
- Delimiter-separated output defaults to comma separated
values (CSV), i.e. all data in one data set is delimited by a comma
character. This option allows one to change the delimiting character to
something else. Note, to switch to tab-separated data, use $'\t' as
delimiting character.
- --csv-noheader
- Do not print header for Delimiter-separated output, such as
CSV
- (default=off)
- Command line options to interact with the structure
constraints feature of this program
-
--maxBPspan=INT
- Set the maximum base pair span
- (default=`-1')
-
-C, --constraint[=<filename>] Calculate
structures subject to constraints.
- (default=`')
- The program reads first the sequence, then a string
containing constraints on the structure encoded with the symbols:
- . (no constraint for this base)
- | (the corresponding base has to be paired
- x (the base is unpaired)
- < (base i is paired with a base j>i)
- > (base i is paired with a base j<i)
- and matching brackets ( ) (base i pairs base j)
- With the exception of "|", constraints will
disallow all pairs conflicting with the constraint. This is usually
sufficient to enforce the constraint, but occasionally a base may stay
unpaired in spite of constraints. PF folding ignores constraints of type
"|".
- --batch
- Use constraints for multiple sequences. (default=off)
- Usually, constraints provided from input file only apply to
a single input sequence. Therefore, RNAcofold will stop its computation
and quit after the first input sequence was processed. Using this switch,
RNAcofold processes multiple input sequences and applies the same provided
constraints to each of them.
- --canonicalBPonly
- Remove non-canonical base pairs from the structure
constraint
- (default=off)
- --enforceConstraint
- Enforce base pairs given by round brackets ( ) in structure
constraint
- (default=off)
-
--shape=<filename>
- Use SHAPE reactivity data to guide structure
predictions
-
--shapeMethod=[D/Z/W] + [optional
parameters]
- Select method to incorporate SHAPE reactivity
- data.
- (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] Select method to convert SHAPE
reactivities to
- pairing probabilities.
- (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 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.
-
-p, --partfunc[=INT]
- Calculate the partition function and base pairing
probability matrix in addition to the mfe structure. Default is
calculation of mfe structure only.
- (default=`1')
- In addition to the MFE structure we print a coarse
representation of the pair probabilities in form of a pseudo bracket
notation, followed by the ensemble free energy, as well as the centroid
structure derived from the pair probabilities together with its free
energy and distance to the ensemble. Finally it prints the frequency of
the mfe structure, and the structural diversity (mean distance between the
structures in the ensemble). See the description of pf_fold() and
mean_bp_dist() and centroid() in the RNAlib documentation for details.
Note that unless you also specify -d2 or -d0, the partition
function and mfe calculations will use a slightly different energy model.
See the discussion of dangling end options below.
- An additionally passed value to this option changes the
behavior of partition function calculation:
- In order to calculate the partition function but not the
pair probabilities
- use the -p0 option and save about
- 50% in runtime. This prints the ensemble free energy
-kT ln(Z).
-
-a, --all_pf[=INT]
- Compute the partition function and free energies not only
of the hetero-dimer consisting of the two input sequences (the "AB
dimer"), but also of the homo-dimers AA and BB as well as A and B
monomers.
- (default=`1')
- The output will contain the free energies for each of these
species, as well as 5 dot plots containing the conditional pair
probabilities, called "ABname5.ps", "AAname5.ps" and
so on. For later use, these dot plot files also contain the free energy of
the ensemble as a comment. Using -a automatically switches on the
-p option. Base pair probability computations may be turned off
altogether by providing "0" as an argument to this parameter. In
that case, no dot plot files will be generated.
-
-c, --concentrations
- In addition to everything listed under the -a
option, read in initial monomer concentrations and compute the expected
equilibrium concentrations of the 5 possible species (AB, AA, BB, A,
B).
- (default=off)
- Start concentrations are read from stdin (unless the
-f option is used) in [mol/l], equilibrium concentrations are given
realtive to the sum of the two inputs. An arbitrary number of initial
concentrations can be specified (one pair of concentrations per
line).
-
-f, --concfile=filename
- Specify a file with initial concentrations for the two
sequences.
- The table consits of arbitrary many lines with just two
numbers (the concentration of sequence A and B). This option will
automatically toggle the -c (and thus -a and -p)
options (see above).
- --centroid
- Compute the centroid structure. (default=off)
- Additionally to the MFE structure, compute the centroid
representative of the structure ensemble. Here, we apply the base pair
distance as distance measure, and report the structure that minimizes its
Boltzmann weighted base pair distance to the rest of the ensemble.
Computing the centroid structure requires equilibrium base pair
probabilities. Therefore, this option implies the -p switch. For
historical reasons, the centroid structure output is deactivated by
default.
-
--MEA[=gamma]
- Calculate an MEA (maximum expected accuracy) structure,
where the expected accuracy is computed from the pair probabilities: each
base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired
base is given by the probability of not forming a pair.
- (default=`1.')
- The parameter gamma tunes the importance of correctly
predicted pairs versus unpaired bases. Thus, for small values of gamma the
MEA structure will contain only pairs with very high probability. Using
--MEA implies -p for computing the pair probabilities.
-
-S, --pfScale=scaling factor
- In the calculation of the pf use scale*mfe 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 long sequences. You can also recompile the program
to use double precision (see the README file).
-
--bppmThreshold=<value>
- Set the threshold for base pair probabilities included in
the postscript output
- (default=`1e-5')
- By setting the threshold the base pair probabilities that
are included in the output can be varied. By default only those exceeding
1e-5 in probability will be shown as squares in the dot plot. Changing the
threshold to any other value allows for increase or decrease of data.
-
-g, --gquad
- Incoorporate G-Quadruplex formation into the structure
prediction algorithm.
- (default=off)
-
-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)
- Mostly for testing.
-
-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 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. RNAcofold -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.
-
--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.
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, Ch. Flamm, P.F. Stadler, I.L. Hofacker, (2006), "Partition
Function and Base Pairing Probabilities of RNA Heterodimers", Algorithms
Mol. 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
Ivo L Hofacker, Peter F Stadler, Stephan Bernhart, Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].