--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAPLFOLD "1" "July 2013" "RNAplfold 2.1.2" "User Commands"
+.SH NAME
+RNAplfold \- manual page for RNAplfold 2.1.2
+.SH SYNOPSIS
+.B RNAplfold
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAplfold 2.1.2
+.PP
+calculate locally stable secondary structure \- pair probabilities
+.PP
+Computes local pair probabilities for base pairs with a maximal span of L. The
+probabilities are averaged over all windows of size L that contain the base
+pair. For a sequence of length n and a window size 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 stable RNA structures.
+.PP
+
+Output consists of a dot plot in postscript file, where the averaged pair probabilities
+can easily be parsed and visually inspected.
+
+The -u option makes i possible to compute the probability that a stretch of x consequtive
+nucleotides is unpaired, which is useful for predicting possible binding sites. Again
+this probability is averaged over all windows containing the region.
+
+.B WARNING! Output format changed!!
+
+The output is a plain text matrix containing on each line a position i followed by the
+probability that i is unpaired, [i-1..i] is unpaired [i-2..i] is unpaired and so on to
+the probability that [i-x+1..i] is unpaired.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Print help and exit
+.TP
+\fB\-\-detailed\-help\fR
+Print help, including all details and hidden
+options, and exit
+.TP
+\fB\-\-full\-help\fR
+Print help, including hidden options, and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Print version and exit
+.SS "General Options:"
+.IP
+Below are command line options which alter the general behavior of this
+program
+.TP
+\fB\-W\fR, \fB\-\-winsize\fR=\fIsize\fR
+Average the pair probabilities over windows of
+given size
+.IP
+(default=`70')
+.TP
+\fB\-L\fR, \fB\-\-span\fR=\fIsize\fR
+Set the maximum allowed separation of a base pair
+to span. I.e. no pairs (i,j) with j\-i > span
+will be allowed. Defaults to winsize if
+parameter is omitted
+.TP
+\fB\-c\fR, \fB\-\-cutoff\fR=\fIFLOAT\fR
+Report only base pairs with an average probability
+> cutoff in the dot plot
+.IP
+(default=`0.01')
+.TP
+\fB\-o\fR, \fB\-\-print_onthefly\fR
+Save memory by printing out everything during
+computation.
+NOTE: activated per default for sequences over
+1M bp.
+.IP
+(default=off)
+.TP
+\fB\-u\fR, \fB\-\-ulength\fR=\fIlength\fR
+Compute the mean probability that regions of
+length 1 to a given length are unpaired. Output
+is saved in a _lunp file.
+.IP
+(default=`31')
+.TP
+\fB\-O\fR, \fB\-\-opening_energies\fR
+Switch output from probabilities to their
+logarithms, which are NOT exactly the mean
+energies needed to the respective stretch of
+bases!
+NOTE: This actives \fB\-u\fR option.
+.IP
+(default=off)
+.TP
+\fB\-\-plex_output\fR
+Create additional output files for RNAplex.
+.IP
+(default=off)
+.TP
+\fB\-\-noconv\fR
+Do not automatically substitude nucleotide "T"
+with "U"
+.IP
+(default=off)
+.SS "Model Details:"
+.TP
+\fB\-T\fR, \fB\-\-temp\fR=\fIDOUBLE\fR
+Rescale energy parameters to a temperature of temp
+C. Default is 37C.
+.TP
+\fB\-4\fR, \fB\-\-noTetra\fR
+Do not include special tabulated stabilizing
+energies for tri\-, tetra\- and hexaloop hairpins.
+Mostly for testing.
+.IP
+(default=off)
+.TP
+\fB\-d\fR, \fB\-\-dangles\fR=\fIINT\fR
+How to treat "dangling end" energies for bases
+adjacent to helices in free ends and multi\-loops
+.IP
+(default=`2')
+.IP
+With \fB\-d2\fR dangling energies will be added for the bases adjacent to a helix on
+both sides in any case.
+.HP
+\fB\-d0\fR ignores dangling ends altogether (mostly for debugging).
+.TP
+\fB\-\-noLP\fR
+Produce structures without lonely pairs (helices
+of length 1).
+.IP
+(default=off)
+.IP
+For partition function folding this only disallows pairs that can only occur
+isolated. Other pairs may still occasionally occur as helices of length 1.
+.TP
+\fB\-\-noGU\fR
+Do not allow GU pairs
+.IP
+(default=off)
+.TP
+\fB\-\-noClosingGU\fR
+Do not allow GU pairs at the end of helices
+.IP
+(default=off)
+.TP
+\fB\-P\fR, \fB\-\-paramFile\fR=\fIparamfile\fR
+Read energy parameters from paramfile, instead of
+using the default parameter set.
+.IP
+A sample parameter file should accompany your distribution.
+See the RNAlib documentation for details on the file format.
+.TP
+\fB\-b\fR, \fB\-\-binaries\fR
+Output accessibility profiles in binary format
+\&. (default=off)
+.IP
+The binary files produced by RNAplfold do not need to be parsed by RNAplex,
+.IP
+so that they are directly loaded into memory. This is useful when large
+sequences have to be searched for putative hybridization sites. An other
+advantage of the binary format is the 50% file size decrease.
+.TP
+\fB\-\-nsp\fR=\fISTRING\fR
+Allow other pairs in addition to the usual
+AU,GC,and GU pairs.
+.IP
+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 \fB\-nsp\fR \fB\-GA\fR will allow GA and AG pairs. Nonstandard pairs are
+given 0 stacking energy.
+.TP
+\fB\-e\fR, \fB\-\-energyModel\fR=\fIINT\fR
+Rarely used option to fold sequences from the
+artificial ABCD... alphabet, where A pairs B,
+C\-D etc. Use the energy parameters for GC (\fB\-e\fR
+1) or AU (\fB\-e\fR 2) pairs.
+.TP
+\fB\-\-betaScale\fR=\fIDOUBLE\fR
+Set the scaling of the Boltzmann factors
+(default=`1.')
+.IP
+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(\fB\-dG\fR/(kT*betaScale)) where k is the
+Boltzmann constant, dG the free energy contribution of the state and T the
+absolute temperature.
+.SH AUTHOR
+
+Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler, Ronny Lorenz
+.SH REFERENCES
+.I 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
+
+
+S. H. Bernhart, I.L. Hofacker, and P.F. Stadler (2006),
+"Local Base Pairing Probabilities in Large RNAs",
+Bioinformatics: 22, pp 614-615
+
+A.F. Bompfuenewerer, R. Backofen, S.H. Bernhart, J. Hertel, I.L. Hofacker, P.F. Stadler, S. Will (2007),
+"Variations on RNA Folding and Alignment: Lessons from Benasque",
+J. Math. Biol.
+
+
+.I 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
+.SH "REPORTING BUGS"
+If in doubt our program is right, nature is at fault.
+.br
+Comments should be sent to rna@tbi.univie.ac.at.
+.SH "SEE ALSO"
+
+RNALfold(1)
git://source.jalview.org / jabaws.git / blobdiff