RNAmultifold - manual page for RNAmultifold 2.5.1
RNAmultifold [
OPTION]... [
FILE]...
RNAmultifold 2.5.1
Compute secondary structures of multiple interacting RNAs
The program works much like RNAfold, but allows one to specify multiple RNA
sequences which are then allowed to form conncected components. 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(s). Multiple strands must be concatenated using
the \'&\' character as separator. RNAmultifold can compute MFE, partition
function, corresponding ensemble free energy and base pairing probabilities.
These properties are either computed for a particular arrangement
(concatenation) of sequences, for the full ensemble of the complex of input
RNAs, or all complexes formed by the input sequences up to a specified number
of interacting sequences. Output consists of a PostScript "dot plot"
file containing the pair probabilities, see the RNAfold man page for details.
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. RNAmultifold 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 RNAmultifold 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, RNAmultifold will not
buffer individual results but print them as soon as they have been
computated.
- --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 RNAmultifold 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, RNAmultifold 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).
- Command line options to interact with the structure
constraints feature of this program
-
--maxBPspan=INT
- Set the maximum base pair span
- (default=`-1')
-
--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. 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
for the complex formed by the input sequences (the "ABC...
mutimer"), but also of all complexes formed by the input sequences up
to the number of input sequences, e.g. AAA, AAB, ABB, BBB, etc.
- (default=`1')
- The output will contain the free energies for each of these
species. Using -a automatically switches on the -p
option.
-
-c, --concentrations
- In addition to everything listed under the -a
option, read in initial monomer concentrations and compute the expected
equilibrium concentrations of all possible species (A, B, AA, BB, AB,
etc).
- (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 inputs. An arbitrary number of initial
concentrations can be specified (one tuple of concentrations per
line).
-
-f, --concfile=filename
- Specify a file with initial concentrations for the input
sequences.
- The table consits of arbitrary many lines with multiple
numbers separated by whitespace (the concentration of the input sequences
A, B, C, etc.). This option will automatically toggle the -c (and
thus -a and -p) options (see above).
-
--absolute-concentrations Report absolute instead of
relative
- concentrations
- (default=off)
-
-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)
- Note, only intramolecular G-quadruplexes are
considered.
-
-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. RNAmultifold -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
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
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].