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.