--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNAPLEX "1" "July 2013" "RNAplex 2.1.2" "User Commands"
+.SH NAME
+RNAplex \- manual page for RNAplex 2.1.2
+.SH SYNOPSIS
+.B RNAplex
+[\fIoptions\fR]
+.SH DESCRIPTION
+RNAplex 2.1.2
+.PP
+Find targets of a query RNA
+.PP
+reads two RNA sequences from stdin or <filename> and computes optimal and
+suboptimal secondary structures for their hybridization. The calculation is
+simplified by allowing only inter\-molecular base pairs. Accessibility effects
+can be estimated by RNAplex if a RNAplfold accessibility profile is provided.
+The computed optimal and suboptimal structure are written to stdout, one
+structure per line. Each line consist of: The structure in dot bracket format
+with a "&" separating the two strands. The range of the structure in the two
+sequences in the format "from,to : from,to"; the energy of duplex structure
+in kcal/mol.
+The format is especially useful for computing the hybrid structure between a
+small probe sequence and a long target sequence.
+.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\-\-version\fR
+Print version and exit
+.SS "Input Options:"
+.IP
+Below are command line options which alter the general input behavior of this
+program
+.TP
+\fB\-q\fR, \fB\-\-query\fR=\fISTRING\fR
+File containing the query sequence.
+.IP
+Input sequences can be given piped to RNAplex or given in a query file with
+the \fB\-q\fR option. Note that the \fB\-q\fR option implies that the \fB\-t\fR option is also
+used
+.TP
+\fB\-t\fR, \fB\-\-target\fR=\fISTRING\fR
+File containing the target sequence.
+.IP
+Input sequences can be given piped to RNAplex or given in a target file with
+the \fB\-t\fR option. Note that the \fB\-t\fR option implies that the \fB\-q\fR option is also
+used
+.TP
+\fB\-a\fR, \fB\-\-accessibility\-dir\fR=\fISTRING\fR
+Location of the accessibility profiles.
+.IP
+This option switches the accessibility modes on and indicates in which
+directory accessibility profiles as generated by RNAplfold can be found
+.TP
+\fB\-b\fR, \fB\-\-binary\fR
+Allow the reading and parsing of memory dumped
+opening energy file
+.IP
+(default=off)
+.IP
+The \fB\-b\fR option allows to read and process opening energy files which are saved
+in binary format
+.IP
+This can reduce by a factor of 500x\-1000x the time needed to process those
+.IP
+files. RNAplex recognizes the corresponding opening energy files by looking
+for files named after the sequence and containing the suffix _openen_bin.
+Please look at the man page of RNAplfold if you need more information on how
+to produce binary opening energy files.
+.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.
+.SS "Algorithms:"
+.IP
+Options which alter the computing behaviour of RNAplex.
+.TP
+\fB\-T\fR, \fB\-\-temp\fR=\fIDOUBLE\fR
+Rescale energy parameters to a temperature T.
+Default is 37C.
+.TP
+\fB\-l\fR, \fB\-\-interaction\-length\fR=\fIINT\fR
+Maximal length of an interaction
+(default=`40')
+.IP
+Maximal allowed length of an interaction
+.TP
+\fB\-c\fR, \fB\-\-extension\-cost\fR=\fIINT\fR
+Cost to add to each nucleotide in a duplex
+(default=`0')
+.IP
+Cost of extending a duplex by one nucleotide. Allows to find compact
+duplexes, having few/small bulges or interior loops Only useful when no
+accessibility profiles are available. This option is disabled if
+accessibility profiles are used (\fB\-a\fR option)
+.TP
+\fB\-p\fR, \fB\-\-probe\-mode\fR
+Compute Tm for probes (default=off)
+.IP
+Use this option if you want to compute the melting temperature of your probes
+.TP
+\fB\-Q\fR, \fB\-\-probe\-concentration\fR=\fIDOUBLE\fR
+Set the probe concentration for the Tm
+.IP
+computation
+.IP
+(default=`0.1')
+.TP
+\fB\-N\fR, \fB\-\-na\-concentration\fR=\fIDOUBLE\fR Set the Na+ concentration for the Tm
+computation
+.IP
+(default=`1.0')
+.TP
+\fB\-M\fR, \fB\-\-mg\-concentration\fR=\fIDOUBLE\fR Set the Mg2+ concentration for the Tm
+computation
+.IP
+(default=`1.0')
+.TP
+\fB\-K\fR, \fB\-\-k\-concentration\fR=\fIDOUBLE\fR
+Set the K+ concentration for the Tm computation
+.IP
+(default=`1.0')
+.TP
+\fB\-U\fR, \fB\-\-tris\-concentration\fR=\fIDOUBLE\fR
+Set the tris+ concentration for the Tm
+.IP
+computation
+.IP
+(default=`1.0')
+.TP
+\fB\-f\fR, \fB\-\-fast\-folding\fR=\fIINT\fR
+Speedup of the target search
+(default=`0')
+.IP
+This option allows to decide if the backtracking has to be done (\fB\-f\fR 0, \fB\-f\fR 2)
+or not (\fB\-f\fR 1). For \fB\-f\fR 0 the structure is computed based on the standard
+energy model. This is the slowest and most precise mode of RNAplex. With \fB\-f\fR
+2, the structure is computed based on the approximated plex model. If a lot
+of targets are returned this is can greatly improve the runtime of RNAplex.
+\fB\-f\fR 1 is the fastest mode, as no structure are recomputed
+.TP
+\fB\-V\fR, \fB\-\-scale\-accessibility\fR=\fIDOUBLE\fR
+Rescale all opening energy by a factor V
+.IP
+(default=`1.0')
+.IP
+Scale\-factor for the accessibility. If V is set to 1 then the scaling has no
+effect on the accessibility.
+.TP
+\fB\-C\fR, \fB\-\-constraint\fR
+Calculate structures subject to constraints.
+(default=off)
+.IP
+The program reads first the sequence, then a string containing constraints on
+the structure for the query sequence encoded with the symbols:
+\&. (no constraint for this base)
+| (the corresponding base has to be paired)
+.TP
+\fB\-A\fR, \fB\-\-alignment\-mode\fR
+Tells RNAplex to compute interactions based on
+alignments
+.IP
+(default=off)
+.IP
+If the A option is set RNAplex expects clustalw files as input for the \fB\-q\fR and
+\fB\-t\fR option.
+.TP
+\fB\-k\fR, \fB\-\-convert\-to\-bin\fR
+If set, RNAplex will convert all opening energy
+file in a directory set by the \fB\-a\fR option into
+binary opening energy files
+.IP
+(default=off)
+.IP
+RNAplex can be used to convert existing text formatted opening energy files
+into binary formatted files. In this mode RNAplex does not compute
+interactions.
+.SS "Output:"
+.IP
+Options that modify the output
+.TP
+\fB\-z\fR, \fB\-\-duplex\-distance\fR=\fIINT\fR
+Distance between target 3' ends of two
+consecutive duplexes
+.IP
+(default=`0')
+.IP
+Distance between the target 3'ends of two consecutive duplexes. Should be set
+to the maximal length of interaction to get good results
+.IP
+Smaller z leads to larger overlaps between consecutive duplexes.
+.TP
+\fB\-e\fR, \fB\-\-energy\-threshold\fR=\fIDOUBLE\fR Minimal energy for a duplex to be returned
+(default=`\-100000')
+.IP
+Energy threshold for a duplex to be returned. The threshold is set on the
+total energy of interaction, i.e. the hybridization energy corrected for
+opening energy if \fB\-a\fR is set or the energy corrected by \fB\-c\fR. If unset, only the
+mfe will be returned
+.TP
+\fB\-I\fR, \fB\-\-produce\-ps\fR=\fISTRING\fR
+Draw an alignment annotated interaction from
+RNAplex
+.IP
+This option allows to produce interaction figures in PS\-format a la
+RNAalifold, where base\-pair conservation is represented in color\-coded
+format. In this mode no interaction are computed, but the \fB\-I\fR option indicates
+the location of the file containing interactions between two RNA
+(alignments/sequence) from a previous run. If the \fB\-A\fR option is not set a
+structure figure a la RNAfold with color\-coded annotation of the
+accessibilities is returned
+.TP
+\fB\-L\fR, \fB\-\-WindowLength\fR=\fIINT\fR
+Tells how large the region around the target
+site should be for redrawing the alignment
+interaction
+.IP
+(default=`1')
+.IP
+This option allow to specify how large the region surrounding the target site
+should be set when generating the alignment figure of the interaction
+.SH AUTHOR
+
+Hakim Tafer, Ivo L. Hofacker
+.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
+
+
+The calculation of duplex structure is based on dynamic programming algorithm originally
+developed by Rehmsmeier and in parallel by Hofacker.
+
+H. Tafer and I.L. Hofacker (2008),
+"RNAplex: a fast tool for RNA-RNA interaction search.",
+Bioinformatics: 24(22), pp 2657-2663
+
+S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster (1993),
+"RNA multi-structure landscapes",
+Euro Biophys J: 22, pp 13-24
+
+.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