Provided by: vienna-rna_2.6.4+dfsg-1build2_amd64 
NAME
RNAsnoop - manual page for RNAsnoop 2.6.4
SYNOPSIS
RNAsnoop [options]
DESCRIPTION
RNAsnoop 2.6.4
Find targets of a query H/ACA snoRNA
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 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.
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.
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.
--help Print help and exit
--detailed-help
Print help, including all details and hidden options, and exit
-V, --version
Print version and exit
I/O Options:
Command line options for input and output (pre-)processing
-s, --query=STRING
File containing the query sequence.
Input sequences can be given piped to RNAsnoop or given in a query file with the -s option. Note
that the -s option implies that the -t option is also used.
-t, --target=STRING
File containing the target sequence.
Input sequences can be given piped to RNAsnoop or given in a target file with the -t optionNote
that the -t option implies that the -s option is also used.
-S, --suffix=STRING
Specificy the suffix that was added by RNAup to the accessibility files.
(default=`_u1_to_30.out')
-P, --from-RNAplfold=STRING
Specify the directory where accessibility profile generated by RNAplfold are found.
-U, --from-RNAup=STRING
Specify the directory where accessibility profiles generated by RNAup are found.
-O, --output_directory=STRING Set where the generated figures should be
stored.
(default=`./')
Algorithms:
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 -2.8(kcal/mol) should be given as -280(decacal/mol).
-A, --alignment-mode
Specify if RNAsnoop gets alignments or single sequences as input.
(default=off)
-f, --fast-folding=INT
Speedup of the target search. (default=`1')
This option allows one to decide if the backtracking has to be done (-f 1) or not (-f 0). For -f 1
the structure is computed based on the standard energy model. This is the slowest mode of
RNAsnoop. -f 0 is the fastest mode, as no structure are recomputed and only the interaction energy
is returned.
-c, --extension-cost=INT
Cost to add to each nucleotide in a duplex. (default=`0')
Cost of extending a duplex by one nucleotide. Allows one 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 (-P option).
-e, --energy-threshold=DOUBLE Maximal energy difference between the mfe and
the desired suboptimal.
(default=`-1')
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 -a is set or the energy corrected by
-c. If unset, only the mfe will be returned.
-o, --minimal-right-duplex=INT
Minimal Right Duplex Energy
(default=`-270')
-l, --minimal-loop-energy=INT Minimal Right Duplex Energy.
(default=`-280')
Minimal Stem Loop Energy of the snoRNA. The energy should be given in decacalories, i.e. a minimal
stem-loop energy of -2.8 kcal/mol corresponds to -280 decacal/mol.
-p, --minimal-left-duplex=INT Minimal Left Duplex Energy.
(default=`-170')
-q, --minimal-duplex=INT
Minimal Duplex Energy.
(default=`-1090')
-d, --duplex-distance=INT
Distance between target 3' ends of two consecutive duplexes.
(default=`2')
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.
-h, --minimal-stem-length=INT Minimal snoRNA stem length.
(default=`5')
-i, --maximal-stem-length=INT Maximal snoRNA stem length.
(default=`120')
-j, --minimal-duplex-box-length=INT
Minimal distance between the duplex end and the
H/ACA box.
(default=`11')
-k, --maximal-duplex-box-length=INT
Maximal distance between the duplex end and the
H/ACA box.
(default=`16')
-m, --minimal-snoRNA-stem-loop-length=INT
Minimal number of nucleotides between the
beginning of stem loop and
beginning of the snoRNA sequence.
(default=`1')
-n, --maximal-snoRNA-stem-loop-length=INT
Maximal number of nucleotides between the
beginning of stem loop and
beginning of the snoRNA sequence.
(default=`100000')
-v, --minimal-snoRNA-duplex-length=INT
Minimal distance between duplex start and
snoRNA.
(default=`0')
-w, --maximal-snoRNA-duplex-length=INT
Maximal distance between duplex start and
snoRNA.
(default=`0')
-x, --minimal-duplex-stem-energy=INT
Minimal duplex stem energy.
(default=`-1370')
-y, --minimal-total-energy=INT
Minimal total energy.
(default=`100000')
-a, --maximal-stem-asymmetry=INT
Maximal snoRNA stem asymmetry.
(default=`30')
-b, --minimal-lower-stem-energy=INT
Minimal lower stem energy.
(default=`100000')
-L, --alignmentLength=INT
Limit the extent of the interactions to L nucleotides.
(default=`25')
Structure Constraints:
Command line options to interact with the structure constraints feature of this program
-C, --constraint
Calculate the stem structure subject to constraints.
(default=off)
The program reads first the stem sequence, then a string containing constraints on the structure
encoded with the symbols:
. (no constraint for this base)
| (the corresponding base has to be paired
x (the base is unpaired)
< (base i is paired with a base j>i)
> (base i is paired with a base j<i)
and matching brackets ( ) (base i pairs base j)
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 "|".
Plotting:
Command line options for changing the default behavior of structure layout and pairing probability
plots.
-I, --produce-ps
Draw annotated 2D structures for a list of dot-bracket structures.
(default=off)
This option allows one to produce interaction figures in PS-format with conservation/accessibility
annotation, if available.
-N, --direct-redraw
Outputs 2D interactions concurrently with the interaction calculation for each suboptimal
interaction. The -I option should be preferred.
(default=off)
REFERENCES
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
R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms
for Molecular Biology 11:1 pp 1-13
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
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
AUTHOR
Hakim Tafer, Ivo L. Hofacker
REPORTING BUGS
If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.
RNAsnoop 2.6.4 January 2025 RNASNOOP(1)