--- /dev/null
+2.1.2
+
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
+.TH RNASNOOP "1" "July 2013" "RNAsnoop 2.1.2" "User Commands"
+.SH NAME
+RNAsnoop \- manual page for RNAsnoop 2.1.2
+.SH SYNOPSIS
+.B RNAsnoop
+[\fIoptions\fR]
+.SH DESCRIPTION
+RNAsnoop 2.1.2
+.PP
+Find targets of a query H/ACA snoRNA
+.PP
+reads a target RNA sequence and a H/ACA snoRNA sequence
+from a target and query file, respectively and computes optimal
+and suboptimal secondary structures for their hybridization. The
+calculation can be done roughly done in O(nm), where is n the length
+of the target sequence and m is the length of the snoRNA stem, as it
+is specially tailored to the special case of H/ACA snoRNA. For general
+purpose target predictions, please have a look at RNAduplex, RNAup,
+RNAcofold and RNAplex. Accessibility effects can be estimated by
+RNAsnoop if a RNAplfold accessibility profile is provided.
+.PP
+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 '<>' brackets represent snoRNA intramolecular
+interactions, while the '()' brackets represent intermolecular
+interactions between the snoRNA and its target.
+.PP
+The range of the structure in the two sequences in the format
+"from,to : from,to"; the energy of duplex structure in
+kcal/mol. If available the opening energy are also returned.
+.TP
+\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
+.SS "Input Options:"
+.IP
+Below are command line options which alter the general input behavior of
+RNAsnoop
+.TP
+\fB\-L\fR, \fB\-\-alignmentLength\fR=\fIINT\fR
+Limit the extent of the interactions to L
+nucleotides (default=`25')
+.TP
+\fB\-C\fR, \fB\-\-constraint\fR
+Calculate the stem structure subject to
+constraints.
+.IP
+(default=off)
+.IP
+The program reads first the stem sequence, then a string containing
+constraints on the structure encoded with the symbols:
+.IP
+\&. (no constraint for this base)
+.IP
+| (the corresponding base has to be paired
+.IP
+x (the base is unpaired)
+.IP
+< (base i is paired with a base j>i)
+.IP
+\f(CW> (base i is paired with a base j<i)\fR
+.IP
+and matching brackets ( ) (base i pairs base j)
+.IP
+With the exception of "|", constraints will disallow all pairs conflicting
+with the constraint. This is usually sufficient to enforce the constraint,
+but occasionally a base may stay unpaired in spite of constraints. PF folding
+ignores constraints of type "|".
+.TP
+\fB\-s\fR, \fB\-\-query\fR=\fISTRING\fR
+File containing the query sequence.
+.IP
+Input sequences can be given piped to RNAsnoop or given in a query file with
+the \fB\-s\fR option. Note that the \fB\-s\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 RNAsnoop or given in a target file with
+the \fB\-t\fR optionNote that the \fB\-t\fR option implies that the \fB\-s\fR option is also used
+.TP
+\fB\-S\fR, \fB\-\-suffix\fR=\fISTRING\fR
+Specificy the suffix that was added by RNAup to
+the accessibility files
+.IP
+(default=`_u1_to_30.out')
+.TP
+\fB\-P\fR, \fB\-\-from\-RNAplfold\fR=\fISTRING\fR
+Specify the directory where accessibility
+profile generated by RNAplfold are found
+.SS "Algorithms:"
+.IP
+Options which alter the computing behaviour of RNAplex.
+Please note that the options allowing to filter out snoRNA\-RNA
+duplexes expect the energy to be given in decacal/mol instead of
+kcal/mol. A threshold of \fB\-2\fR.8(kcal/mol) should be given as \fB\-280\fR(decacal/mol)
+.TP
+\fB\-A\fR, \fB\-\-alignment\-mode\fR
+Specify if RNAsnoop gets alignments or single
+sequences as input
+.IP
+(default=off)
+.TP
+\fB\-f\fR, \fB\-\-fast\-folding\fR=\fIINT\fR
+Speedup of the target search (default=`1')
+.IP
+This option allows to decide if the backtracking has to be
+done (\fB\-f\fR 1) or not (\fB\-f\fR 0). For \fB\-f\fR 1 the structure is computed based
+on the standard energy model. This is the slowest mode of RNAsnoop. \fB\-f\fR
+0 is the fastest mode, as no structure are recomputed and only the
+interaction energy is returned
+.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\-P\fR option)
+.TP
+\fB\-o\fR, \fB\-\-minimal\-right\-duplex\fR=\fIINT\fR
+Minimal Right Duplex Energy
+.IP
+(default=`\-270')
+.TP
+\fB\-l\fR, \fB\-\-minimal\-loop\-energy\fR=\fIINT\fR Minimal Right Duplex Energy
+(default=`\-280')
+.IP
+Minimal Stem Loop Energy of the snoRNA. The energy should be
+given in decacalories, i.e. a minimal stem\-loop energy of \fB\-2\fR.8
+kcal/mol corresponds to \fB\-280\fR decacal/mol
+.HP
+\fB\-p\fR, \fB\-\-minimal\-left\-duplex\fR=\fIINT\fR Minimal Left Duplex Energy
+.IP
+(default=`\-170')
+.TP
+\fB\-q\fR, \fB\-\-minimal\-duplex\fR=\fIINT\fR
+Minimal Duplex Energy
+.IP
+(default=`\-1090')
+.TP
+\fB\-d\fR, \fB\-\-duplex\-distance\fR=\fIINT\fR
+Distance between target 3' ends of two
+consecutive duplexes
+.IP
+(default=`2')
+.IP
+Distance between the target 3'ends of two consecutive
+duplexes. Should be set to the maximal length of interaction to get
+good results. Smaller d leads to larger overlaps between consecutive
+duplexes
+.HP
+\fB\-h\fR, \fB\-\-minimal\-stem\-length\fR=\fIINT\fR Minimal snoRNA stem length
+.IP
+(default=`5')
+.HP
+\fB\-i\fR, \fB\-\-maximal\-stem\-length\fR=\fIINT\fR Maximal snoRNA stem length
+.IP
+(default=`120')
+.TP
+\fB\-j\fR, \fB\-\-minimal\-duplex\-box\-length\fR=\fIINT\fR
+Minimal distance between the duplex end and the
+.IP
+H/ACA box
+.IP
+(default=`11')
+.TP
+\fB\-k\fR, \fB\-\-maximal\-duplex\-box\-length\fR=\fIINT\fR
+Maximal distance between the duplex end and the
+.IP
+H/ACA box
+.IP
+(default=`16')
+.TP
+\fB\-m\fR, \fB\-\-minimal\-snoRNA\-stem\-loop\-length\fR=\fIINT\fR
+Minimal number of nucleotides between the
+.IP
+beginning of stem loop and
+beginning of the snoRNA sequence
+.IP
+(default=`1')
+.TP
+\fB\-n\fR, \fB\-\-maximal\-snoRNA\-stem\-loop\-length\fR=\fIINT\fR
+Maximal number of nucleotides between the
+.IP
+beginning of stem loop and
+beginning of the snoRNA sequence
+.IP
+(default=`100000')
+.TP
+\fB\-v\fR, \fB\-\-minimal\-snoRNA\-duplex\-length\fR=\fIINT\fR
+Minimal distance between duplex start and
+.IP
+snoRNA
+.IP
+(default=`0')
+.TP
+\fB\-w\fR, \fB\-\-maximal\-snoRNA\-duplex\-length\fR=\fIINT\fR
+Maximal distance between duplex start and
+.IP
+snoRNA
+.IP
+(default=`0')
+.TP
+\fB\-x\fR, \fB\-\-minimal\-duplex\-stem\-energy\fR=\fIINT\fR
+Minimal duplex stem energy
+.IP
+(default=`\-1370')
+.TP
+\fB\-y\fR, \fB\-\-minimal\-total\-energy\fR=\fIINT\fR
+Minimal total energy
+.IP
+(default=`100000')
+.TP
+\fB\-a\fR, \fB\-\-maximal\-stem\-asymmetry\fR=\fIINT\fR
+Maximal snoRNA stem asymmetry
+.IP
+(default=`30')
+.TP
+\fB\-b\fR, \fB\-\-minimal\-lower\-stem\-energy\fR=\fIINT\fR
+Minimal lower stem energy
+.IP
+(default=`100000')
+.SS "Output options:"
+.IP
+Options that modifies the output
+.TP
+\fB\-e\fR, \fB\-\-energy\-threshold\fR=\fIDOUBLE\fR Maximal energy difference between the mfe and
+the desired suboptimal
+.IP
+(default=`\-1')
+.IP
+Energy range for a duplex to be returned. The threshold is set on the total
+energy of interaction, i.e. the hybridizationenergy 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
+Draw annotated 2D structures for a list of
+dot\-bracket structures
+.IP
+(default=off)
+.IP
+This option allows to produce interaction figures in PS\-format with
+conservation/accessibility annotation, if available
+.TP
+\fB\-O\fR, \fB\-\-output_directory\fR=\fISTRING\fR Set where the generated figures should be
+stored
+.IP
+(default=`./')
+.TP
+\fB\-N\fR, \fB\-\-direct\-redraw\fR
+Outputs 2D interactions concurrently with the
+interaction calculation for each suboptimal
+interaction. The \fB\-I\fR option should be
+preferred.
+.IP
+(default=off)
+.TP
+\fB\-U\fR, \fB\-\-from\-RNAup\fR=\fISTRING\fR
+Specify the directory where accessibility
+profiles generated by RNAup are found
+.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, S. Kehr, J. Hertel, I.L. Hofacker, P.F. Stadler (2009),
+"RNAsnoop: efficient target prediction for H/ACA snoRNAs.",
+Bioinformatics: 26(5), pp 610-616
+
+.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.
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