Provided by: vienna-rna_2.4.17+dfsg-2build2_amd64 
NAME
RNAcofold - manual page for RNAcofold 2.4.17
SYNOPSIS
RNAcofold [OPTION]... [FILE]...
DESCRIPTION
RNAcofold 2.4.17
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
General Options:
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)
Structure Constraints:
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.
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.
-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)
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.
(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.
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, 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
AUTHOR
Ivo L Hofacker, Peter F Stadler, Stephan Bernhart, 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.