Provided by: vienna-rna_2.4.17+dfsg-2build2_amd64 
NAME
RNAsnoop - manual page for RNAsnoop 2.4.17
SYNOPSIS
RNAsnoop [options]
DESCRIPTION
RNAsnoop 2.4.17
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
Input Options:
Below are command line options which alter the general input behavior of RNAsnoop
-L, --alignmentLength=INT
Limit the extent of the interactions to L nucleotides
(default=`25')
-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 "|".
-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
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)
-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')
Output options:
Options that modifies the output
-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
-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
-O, --output_directory=STRING Set where the generated figures should be
stored
(default=`./')
-N, --direct-redraw
Outputs 2D interactions concurrently with the interaction calculation for each
suboptimal interaction. The -I option should be preferred.
(default=off)
-U, --from-RNAup=STRING
Specify the directory where accessibility profiles generated by RNAup are found
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.