Provided by: vienna-rna_2.6.4+dfsg-1build1_amd64 
NAME
RNALalifold - manual page for RNALalifold 2.6.4
SYNOPSIS
RNALalifold [options] <file1.aln>
DESCRIPTION
RNALalifold 2.6.4
calculate locally stable secondary structures for a set of aligned RNAs
reads aligned RNA sequences from stdin or file.aln and calculates 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.
-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)
-q, --quiet
Be quiet. (default=off)
This option can be used to minimize the output of additional information and
non-severe warnings which otherwise might spam stdout/stderr.
I/O Options:
Command line options for input and output (pre-)processing
-f, --input-format=C|S|F|M
File format of the input multiple sequence alignment (MSA).
If this parameter is set, the input is considered to be in a particular file
format. Otherwise, the program tries to determine the file format automatically, if
an input file was provided in the set of parameters. In case the input MSA is
provided in interactive mode, or from a terminal (TTY), the programs default is to
assume CLUSTALW format. Currently, the following formats are available: ClustalW
('C'), Stockholm 1.0 ('S'), FASTA/Pearson ('F'), and MAF ('M').
--csv Create comma separated output (csv)
(default=off)
--aln[=prefix]
Produce output alignments and secondary structure plots for each hit found.
This option tells the program to produce, for each hit, a colored and structure
annotated (sub)alignment and secondary structure plot in PostScript format. It also
adds the subalignment hit into a multi-Stockholm formatted file
"RNALalifold_results.stk". The postscript output file names are "aln_start_end.eps"
and "ss_start_end.eps". All files will be created in the current directory. The
optional argument string can be used to set a specific prefix that is used to name
the output files. The file names then become "prefix_aln_start_end.eps",
"prefix_ss_start_end.eps", and "prefix.stk". Note: Any special characters in the
prefix 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)
--aln-stk[=prefix]
Add hits to a multi-Stockholm formatted output file.
(default=`RNALalifold_results')
The default file name used for the output is "RNALalifold_results.stk". Users may
change the filename to "prefix.stk" by specifying the prefix as optional argument.
The file will be create in the current directory if it does not already exist. In
case the file already exists, output will be appended to it. Note: Any special
characters in the prefix 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)
--mis Output "most informative sequence" instead of simple consensus: For each column of
the alignment output the set of nucleotides with frequency greater than average in
IUPAC notation.
(default=off)
--split-contributions
Split the free energy contributions into separate parts
(default=off)
By default, only the total energy contribution for each hit is returned. Using
this option, this contribution is split into individual parts, i.e. the Nearest
Neighbor model energy, the covariance pseudo energy, and if applicable, a remaining
pseudo energy derived from special constraints, such as probing signals like SHAPE.
--noconv
Do not automatically substitute nucleotide "T" with "U".
(default=off)
--auto-id
Automatically generate an ID for each alignment.
(default=off)
The default mode of RNALalifold is to automatically determine an ID from the input
alignment if the input file format allows to do that. Alignment IDs are, for
instance, usually given in Stockholm 1.0 formatted input. If this flag is active,
RNALalifold ignores any IDs retrieved from the input and automatically generates an
ID for each alignment.
--id-prefix=STRING
Prefix for automatically generated IDs (as used in output file names).
(default=`alignment')
If this parameter is set, each alignment 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_aln.ps"
(annotated alignment), etc. where xxxx is the alignment number beginning with the
second alignment in the input. Use this setting in conjunction with the
--continuous-ids flag to assign IDs beginning with the first input alignment.
--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].
--id-start=LONG
Specify the first number in automatically generated alignment IDs.
(default=`1')
When alignment 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 continuous alignment IDs, i.e. it activates the --continuous-ids
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 '>'.
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, --maxBPspan=INT
Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with
j-i>span will be allowed.
(default=`70')
--threshold=DOUBLE
Energy threshold in kcal/mol per nucleotide above which secondary structure hits
are omitted in the output.
(default=`-0.1')
-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=file1,file2
Use SHAPE reactivity data to guide structure predictions.
Multiple shapefiles for the individual sequences in the alignment may be specified
as a comma separated list. An optional association of particular shape files to a
specific sequence in the alignment can be expressed by prepending the sequence
number to the filename, e.g. "5=seq5.shape,3=seq3.shape" will assign the
reactivity values from file seq5.shape to the fifth sequence in the alignment, and
the values from file seq3.shape to sequence 3. If no assignment is specified, the
reactivity values are assigned to corresponding sequences in the order they are
given.
--shapeMethod=D[mX][bY]
Specify the method how to convert SHAPE reactivity data to pseudo energy
contributions.
(default=`D')
Currently, the only data conversion method available is that of to Deigan et al
2009. This method is the default and 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 as stated in the paper mentionen before. 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".
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.
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 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)
--cfactor=DOUBLE
Set the weight of the covariance term in the energy function
(default=`1.0')
--nfactor=DOUBLE
Set the penalty for non-compatible sequences in the covariance term of the energy
function
(default=`1.0')
-R, --ribosum_file=ribosumfile
use specified Ribosum Matrix instead of normal
energy model.
Matrixes to use should be 6x6 matrices, the order of the terms is 'AU', 'CG', 'GC',
'GU', 'UA', 'UG'.
-r, --ribosum_scoring
use ribosum scoring matrix. (default=off)
The matrix is chosen according to the minimal and maximal pairwise identities of
the sequences in the 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.
--nsp="-GA" will allow GA and AG pairs. Nonstandard pairs are given 0 stacking
energy.
-e, --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 (-e 1) or AU (-e 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.
Plotting:
Command line options for changing the default behavior of structure layout and
pairing probability plots
--aln-EPS[=prefix]
Produce colored and structure annotated subalignment for each hit.
The default file name used for the output is "aln_start_end.eps" where "start" and
"end" denote the first and last column of the subalignment relative to the input
(1-based). Users may change the filename to "prefix_aln_start_end.eps" by
specifying the prefix as optional argument. Files will be create in the current
directory. Note: Any special characters in the prefix 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)
--aln-EPS-cols=INT
Number of columns in colored EPS alignment output.
(default=`60')
A value less than 1 indicates that the output should not be wrapped at all.
--aln-EPS-ss[=prefix]
Produce colored consensus secondary structure plots in PostScript format.
The default file name used for the output is "ss_start_end.eps" where "start" and
"end" denote the first and last column of the subalignment relative to the input
(1-based). Users may change the filename to "prefix_ss_start_end.eps" by specifying
the prefix as optional argument. Files will be create in the current directory.
Note: Any special characters in the prefix 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)
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
Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F.
Stadler (2008), "RNAalifold: Improved consensus structure prediction for RNA alignments",
BMC Bioinformatics: 9, pp 474
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, 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.