RNApaln - manual page for RNApaln 2.5.1
RNApaln [
OPTION]...
RNApaln 2.5.1
RNA alignment based on sequence base pairing propensities
Uses string-alignment techniques to perform fast pairwise structural alignments
of RNAs. Similar to RNApdist secondary structure is incorporated in an
approximate manner by computing base pair probabilities, which are then
reduced to a vector holding the probability that a base is paired upstream,
downstream, or remains unpaired. Such pair propsensity vectors can then be
compared using standard alignment algorithms. In contrast to RNApdist, RNApaln
performs similarity (instead of distance) alignments, considers both sequence
and structure information, and uses affine (rather than linear) gap costs.
RNApaln can perform semi-local alignments by using free end gaps, a true local
alignment mode is planned.
The same approach has since been used in the StraL program from Gerhard
Steeger's group. Since StraL has optimized parameters and a multiple alignment
mode, it be be currently the better option.
-
-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
- Below are command line options which alter the general
behavior of this program
-
-B, --printAlignment[=filename]
- Print an "alignment" with gaps of the
- profiles
- The aligned structures are written to filename, if
specified Otherwise output is written to stdout, unless the -Xm
option is set in which case "backtrack.file" is used.
- (default=`stdout')
- The following symbols are used:
- (
- ) essentially upstream (downstream) paired bases
- {
- } weakly upstream (downstream) paired bases
- |
- strongly paired bases without preference
- ,
- weakly paired bases without preference
- .
- essentially unpaired bases.
- --noconv
- Do not automatically substitude nucleotide "T"
with "U"
- (default=off)
- Select additional algorithms which should be included in
the calculations.
-
-X, --mode=pmfc
- Set the alignment mode to be used
- The alignment mode is passed as a single character value.
The following options are available: 'p' - Compare the structures
pairwise, that is first with 2nd, third with 4th etc. This is the
default.
- 'm'
- - Calculate the distance matrix between all structures. The
output is
- formatted as a lower triangle matrix.
- 'f' - Compare each structure to the first one.
- 'c' - Compare continuously, that is i-th with (i+1)th
structure.
-
--gapo=open
- Set the gap open penalty
-
--gape=ext
- Set the gap extension penalty
-
--seqw=w
- Set the weight of sequence (compared to structure) in the
scoring function.
- --endgaps
- Use free end-gaps
- (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. Mostly for testing.
- (default=off)
-
-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. 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.
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
Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P (1993), "RNA
multi-structure landscapes", Euro Biophys J: 22, pp 13-24
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
Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].