RNAalifold - manual page for RNAalifold 2.5.1
RNAalifold [
options] [
<input0.aln>]
[
<input1.aln>]...
RNAalifold 2.5.1
calculate secondary structures for a set of aligned RNAs
Read aligned RNA sequences from stdin or file.aln and calculate their minimum
free energy (mfe) structure, partition function (pf) and base pairing
probability matrix. Currently, input alignments have to be in CLUSTAL,
Stockholm, FASTA, or MAF format. The input format must be set manually in
interactive mode (default is Clustal), but will be determined automagically
from the input file, if not expplicitly set. It returns the mfe structure in
bracket notation, its energy, the free energy of the thermodynamic ensemble
and the frequency of the mfe structure in the ensemble to stdout. It also
produces Postscript files with plots of the resulting secondary structure
graph ("alirna.ps") and a "dot plot" of the base pairing
matrix ("alidot.ps"). The file "alifold.out" will contain
a list of likely pairs sorted by credibility, suitable for viewing with
"AliDot.pl". Be warned that output file will overwrite any existing
files of the same name.
-
-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)
-
-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.
-
-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 alignment at a time. Using this switch, a user can
instead start the computation for many alignments in the input in
parallel. RNAalifold will create as many parallel computation slots as
specified and assigns input alignments 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 RNAalifold 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, RNAalifold 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)
- --color
- Produce a colored version of the consensus structure plot
"alirna.ps" (default b&w only)
- (default=off)
- --aln
- Produce a colored and structure annotated alignment in
PostScript format in the file "aln.ps" in the current
directory.
- (default=off)
-
--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-stk[=prefix]
- Create a multi-Stockholm formatted output file.
(default=`RNAalifold_results')
- The default file name used for the output is
"RNAalifold_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 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)
-
-t, --layout-type=INT
- Choose the layout algorithm. Simple radial layout if 0, or
naview if 1
- (default=`1')
- --noPS
- Do not produce postscript drawing of the mfe
structure.
- (default=off)
- --noDP
- Do not produce dot-plot postscript file containing base
pair or stack probabilitities.
- (default=off)
- In combination with the -p option, this flag
turns-off creation of individual dot-plot files. Consequently, computed
base pair probability output is omitted but centroid and MEA structure
prediction is still performed.
-
-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).
-
-n, --continuous-ids
- Use continuous alignment ID numbering when no alignment ID
can be retrieved from input data.
- (default=off)
- Due to its past, RNAalifold produces a specific set of
output file names for the first input alignment, "alirna.ps",
"alidot.ps", etc. But for all further alignments in the input,
it usually adopts a naming scheme based on IDs, which may be retrieved
from the input alignment's meta-data, or generated by a prefix followed by
an increasing counter. Setting this flag instructs RNAalifold to use the
ID naming scheme also for the first alignment.
- --auto-id
- Automatically generate an ID for each alignment.
- (default=off)
- The default mode of RNAalifold 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, RNAalifold ignores any IDs
retrieved from the input and automatically generates an ID for each
alignment.
-
--id-prefix=prefix
- 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=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].
-
--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=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 '>'.
- 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.
- The constraining structure will be read from 'stdin', the
alignment has to be given as a file name on the command line.
- (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 all alignment records.
(default=off)
- Usually, constraints provided from input file are only
applied to a single sequence alignment. Therefore, RNAalifold will stop
its computation and quit after the first input alignment was processed.
Using this switch, RNAalifold processes all sequence alignments in the
input and applies the same provided constraints to each of them.
- --enforceConstraint
- Enforce base pairs given by round brackets ( ) in structure
constraint
- (default=off)
- --SS_cons
- Use consensus structures from Stockholm file (#=GF SS_cons)
as constraint
- (default=off)
- Stockholm formatted alignment files have the possibility to
store a secondary structure string in one of if ("#=GC") column
annotation meta tags. The corresponding tag name is usually
"SS_cons", a consensus secondary structure. Activating this flag
allows one to use this consensus secondary structure from the input file
as structure constraint. Currently, only the following characters are
interpreted:
- ( ) [mathing parenthesis: column i pairs with column
j]
- < > [matching angular brackets: column i pairs with
column j]
- All other characters are not interpreted (yet). Note:
Activating this flag implies --constraint.
-
--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".
- 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.
- An additionally passed value to this option changes the
behavior of partition function calculation: -p0 deactivates the
calculation of the pair probabilities, saving about 50% in runtime. This
prints the ensemble free energy -kT ln(Z).
-
--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.
- --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)
-
-s, --stochBT=INT
- Stochastic backtrack. Compute a certain number of random
structures with a probability dependend on the partition function. See
-p option in RNAsubopt.
-
--stochBT_en=INT
- same as "-s" but also print out the energies and
probabilities of the backtraced structures.
-
-N, --nonRedundant
- Enable non-redundant sampling strategy.
- (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).
-
-c, --circ
- Assume a circular (instead of linear) RNA molecule.
- (default=off)
-
--bppmThreshold=<value>
- Set the threshold for base pair probabilities included in
the postscript output
- (default=`1e-6')
- 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)
- --sci
- Compute the structure conservation index (SCI) for the MFE
consensus structure of the alignment
- (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 -d2 dangling energies will be added for the
bases adjacent to a helix on both sides
- in any case.
- The option -d0 ignores dangling ends altogether
(mostly for debugging).
- --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')
-
-E, --endgaps
- Score pairs with endgaps same as gap-gap pairs.
- (default=off)
-
-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. The matrix is chosen according
to the minimal and maximal pairwise identities of the sequences in the
file.
- (default=off)
- --old
- use old energy evaluation, treating gaps as
characters.
- (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. RNAfold -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/(kTn*betaScale)) where k is the Boltzmann constant, dG the free
energy contribution of the state, T the absolute temperature and n the
number of sequences.
Caveats:
Sequences are not weighted. If possible, do not mix very similar and dissimilar
sequences. Duplicate sequences, for example, can distort the prediction.
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 algorithm is a variant of the dynamic programming algorithms of M. Zuker and
P. Stiegler (mfe) and J.S. McCaskill (pf) adapted for sets of aligned
sequences with covariance information.
Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler (2002), "Secondary
Structure Prediction for Aligned RNA Sequences", J.Mol.Biol.: 319, pp
1059-1066.
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
A simple call to compute consensus MFE structure, ensemble free energy, base
pair probabilities, centroid structure, and MEA structure for a multiple
sequence alignment (MSA) provided as Stockholm formatted file alignment.stk
might look like:
$ RNAalifold -p --MEA alignment.stk
Consider the following MSA file for three sequences
# STOCKHOLM 1.0
#=GF AC RF01293
#=GF ID ACA59
#=GF DE Small nucleolar RNA ACA59
#=GF AU Wilkinson A
#=GF SE Predicted; WAR; Wilkinson A
#=GF SS Predicted; WAR; Wilkinson A
#=GF GA 43.00
#=GF TC 44.90
#=GF NC 40.30
#=GF TP Gene; snRNA; snoRNA; HACA-box;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR snoRNABase; ACA59;
#=GF DR SO; 0001263; ncRNA_gene;
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0005730; nucleolus;
#=GF RN [1]
#=GF RM 15199136
#=GF RT Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL Mol Cell Biol. 2004;24:5797-5807.
#=GF WK Small_nucleolar_RNA
#=GF SQ 3
AL031296.1/85969-86120 CUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACAGCU
AANU01225121.1/438-603 CUGCCUCACAACAUUUGUGCCUCAGUUACUCAUAGAUGUAGUGAGGGUGACAAUACUUACUCUCGUUGGUGAUAAGGAACAGCU
AAWR02037329.1/29294-29150 ---CUCGACACCACU---GCCUCGGUUACCCAUCGGUGCAGUGCGGGUAGUAGUACCAAUGCUAAUUAGUUGUGAGGACCAACU
#=GC SS_cons -----((((,<<<<<<<<<___________>>>>>>>>>,,,,<<<<<<<______>>>>>>>,,,,,))))::::::::::::
#=GC RF CUGCcccaCAaCacuuguGCCUCaGUUACcCauagguGuAGUGaGgGuggcAaUACccaCcCucgUUgGuggUaAGGAaCAgCU
//
Then, the above program call will produce this output:
3 sequences; length of alignment 84.
>ACA59
CUGCCUCACAACAUUUGUGCCUCAGUUACCCAUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACAGCU
...((((((.(((((((((...........))))))))).))))))..........(((((......)))))............ (-12.54 = -12.77 + 0.23)
...((((((.(((((((((...........))))))))).)))))){{,.......{{{{,......}))))............ [-14.38]
...((((((.(((((((((...........))))))))).))))))..........((((........))))............ {-12.44 = -12.33 + -0.10 d=10.94}
...((((((.(((((((((...........))))))))).))))))..........((((........))))............ {-12.44 = -12.33 + -0.10 MEA=66.65}
frequency of mfe structure in ensemble 0.368739; ensemble diversity 17.77
Here, the first line is written to
stderr and simply states the number of
sequences and the length of the alignment. This line can be suppressed using
the
--quiet option. The main output then consists of 7 lines, where the
first two resemble the FASTA header with the ID as read from the input data
set, followed by the consensus sequence in the second line. The third line
consists of the consensus secondary structure in dot-bracket notation followed
by the averaged minimum free energy in parenthesis. This energy is composed of
two major contributions, the actual free energies derived from the Nearest
Neighbor model, and the covariance pseudo-energy term, which are both
displayed after the equal sign. The fourth line shows the base pair propensity
in pseudo dot-bracket notation followed by the ensemble free energy dG = -kT
ln(Z) in square brackets. Similarly, the next two lines state the controid-
and the MEA structure in dot-bracket notation, followed by their corresponding
free energy contributions, the mean distance (d) to the ensemble as well as
the maximum expected accuracy (MEA). Again, the free energies are split into
Nearest Neighbor contribution and the covariance pseudo-energy term.
Furthermore, RNAalifold will produce three output files: ACA59_ss.ps,
ACA59_dp.ps, and ACA59_ali.out that contain the secondary structure drawing,
the base pair probability dot-plot, and a detailed table of base pair
probabilities, respectively.
When computing base pair probabilities (
--partfunc option), RNAalifold
will produce a file with the suffix `ali.out`. This file contains the base
pairing probabilities between different alignment columns together with some
detailed statistics for the individual sequences within the alignment. The
file is a simple text file with a two line header that states the number of
sequences and length of the alignment. The first couple of lines of this file
may look like:
3 sequence; length of alignment 84
alifold output
14 36 0 92.7% 0.212 CG:1 UA:2
13 37 0 92.7% 0.218 GU:1 AU:2
12 38 0 92.7% 0.231 CG:3
15 35 0 91.9% 0.239 UG:3
16 34 0 85.2% 0.434 UA:2 --:1
8 42 0 80.7% 0.526 AU:3 +
9 41 0 80.4% 0.542 CG:3 +
7 43 1 80.1% 0.541 CG:2 +
Starting with the third row, there are at least six and at most 13 columns
separated by whitespaces stating: (1) the i-position and (2) the j-position of
a potential base pair (i, j), followed by (3) the number of counter examples,
i.e. the number of sequences in the alignment that can't form a canonical base
pair with their respective sequence positions. Next is (4) the base pair
probabilitiy in percent, (5) a pseudo entropy measure S_ij = S_i + S_j - p_ij
ln(p_ij), where S_i and S_j are the positional entropies for the two alignment
columns i and j, and p_ij is the base pair probability. Finally, the last
columns (6-12) state the number of particular base pairs for the individual
sequences in the alignment. Here, we distinguish the base pairs
"GC","CG","AU","UA","GU","UG",
and the special case "--" that represents gaps at both positions i
and j. Finally, base pairs that are not part of the MFE structure are marked
by an additional "+" sign in the last column.
Ivo L Hofacker, Stephan Bernhart, Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].
The ALIDOT package
http://www.tbi.univie.ac.at/RNA/Alidot/