Provided by: vienna-rna_2.6.4+dfsg-1build2_amd64 
NAME
RNApdist - manual page for RNApdist 2.6.4
SYNOPSIS
RNApdist [OPTION]...
DESCRIPTION
RNApdist 2.6.4
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
I/O Options:
Command line options for input and output (pre-)processing
--noconv
Do not automatically substitute nucleotide "T" with "U".
(default=off)
Algorithms:
Select additional algorithms which should be included in the calculations.
-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.
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. When passing the placeholder file name "DNA",
DNA parameters are loaded 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
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)
--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
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.
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
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
AUTHOR
Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer.
REPORTING BUGS
If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.
RNApdist 2.6.4 January 2025 RNAPDIST(1)