--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAPKPLEX "1" "July 2013" "RNAPKplex 2.1.2" "User Commands"
+.SH NAME
+RNAPKplex \- manual page for RNAPKplex 2.1.2
+.SH SYNOPSIS
+.B RNAPKplex
+[\fIOPTIONS\fR]...
+.SH DESCRIPTION
+RNAPKplex 2.1.2
+.PP
+predicts RNA secondary structures including pseudoknots
+.PP
+Computes RNA secondary structures by first making two sequence intervals
+accessible and unpaired using the algorithm of RNAplfold and then calculating
+the energy of the interaction of those two intervals. The algorithm uses
+O(n^2*w^4) CPU time and O(n*w^2) memory space.
+The algorithm furthermore always considers dangle=2 model.
+.PP
+
+It also produces a PostScript file with a plot of the pseudoknot-free
+secondary structure graph, in which the bases forming the pseuodknot
+are marked red.
+
+Sequences are read in a simple text format where each sequence occupies
+a single line. Each sequence may be preceded by a line of the form
+.nf
+.ft CW
+> name
+.ft
+.fi
+to assign a name to the sequence. If a name is given in the input, the
+ PostScript file "name.ps" is produced for the structure graph. Other-
+wise the file name defaults to PKplex.ps. Existing files of the same
+name will be overwritten.
+The input format is similar to fasta except that even long sequences
+may not be interrupted by line breaks, and the header lines are
+optional. The program will continue to read new sequences until a line
+consisting of the single character @ or an end of file condition is
+encountered.
+.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\-V\fR, \fB\-\-version\fR
+Print version and exit
+.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\-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 stabilizing energies for
+certain tetra\-loops. Mostly for testing.
+.IP
+(default=off)
+.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\-\-noconv\fR
+Do not automatically substitude nucleotide "T"
+with "U"
+.IP
+(default=off)
+.TP
+\fB\-\-nsp\fR=\fISTRING\fR
+Allow other pairs in addition to the usual
+AU,GC,and GU pairs.
+.IP
+(default=`empty')
+.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\-\-energyCutoff\fR=\fIDOUBLE\fR
+Energy cutoff or pseudoknot initiation cost.
+Minimum energy gain of a pseudoknot interaction
+for it to be returned. Pseudoknots with smaller
+energy gains are rejected.
+.IP
+(default=`\-8.10')
+.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\-v\fR, \fB\-\-verbose\fR
+print verbose output
+(default=off)
+.TP
+\fB\-s\fR, \fB\-\-subopts\fR=\fIDOUBLE\fR
+print suboptimal structures whose energy
+difference of the pseudoknot to the optimum
+pseudoknot is smaller than the given value.
+.IP
+(default=`0.0')
+.IP
+NOTE: The final energy of a structure is calculated as the sum of the
+pseudoknot interaction energy, the penalty for initiating a pseudoknot and
+the energy of the pseudoknot\-free part of the structure. The \fB\-s\fR option only
+takes the pseudoknot interaction energy into account, so the final energy
+differences may be bigger than the specified value (default=0.).
+.SH AUTHOR
+
+Wolfgang Beyer
+.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
+
+
+.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.
git://source.jalview.org / jabaws.git / blobdiff