RNApdist - manual page for RNApdist 2.5.1
RNApdist [
OPTION]...
RNApdist 2.5.1
Calculate distances between thermodynamic RNA secondary structures ensembles
This program reads RNA sequences from stdin and calculates structure distances
between the thermodynamic ensembles of their secondary structures.
To do this the partition function and matrix of base pairing probabilities is
computed for each sequence. The probability matrix is then condensed into a
vector holding for each base the probabilities of being unpaired, paired
upstream, or paired downstream, respectively. These profiles are compared by a
standard alignment algorithm.
The base pair probabilities are also saved as postscript "dot plots"
(as in RNAfold) in the files "name_dp.ps", where name is the name of
the sequence, or a number if unnamed.
-
-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
- --noconv
- Do not automatically substitude nucleotide "T"
with "U"
- (default=off)
-
-X, --compare=p|m|f|c
- Specify the comparison directive. (default=`p')
- Possible arguments for this option are: -Xp compare
the structures pairwise (p), i.e. first with 2nd, third with 4th etc.
-Xm calculate the distance matrix between all structures. The
output is formatted as a lower triangle matrix. -Xf compare each
structure to the first one. -Xc compare continuously, that is i-th
with (i+1)th structure.
-
-B, --backtrack[=<filename>]
- Print an "alignment" with gaps of the profiles.
The aligned structures are written to <filename>, if specified.
- (default=`none')
- Within the profile output, the following symbols will be
used:
- ()
- essentially upstream (downstream) paired bases
- {}
- weakly upstream (downstream) paired bases
- |
- strongly paired bases without preference
- ,
- weakly paired bases without preference
- .
- essentially unpaired bases.
- If <filename> is not specified, the output is written
to stdout, unless the
- "-Xm" option is set in which case
"backtrack.file" is used.
-
-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
- set energy model for treatment of dangling bases
- (possible values="0", "2"
default=`2')
- --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
S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster (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].