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RNASNOOP(1) User Commands RNASNOOP(1) NAME RNAsnoop - manual page for RNAsnoop 2.7.2 SYNOPSIS RNAsnoop [options] DESCRIPTION RNAsnoop 2.7.2 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 esti- mated 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 for- mat with a '&' separating the two strands. The '<>' brackets represent snoRNA intramolecular interactions, while the '()' brackets represent in- termolecular 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 --full-help Print help, including hidden options, and exit -V, --version Print version and exit --verbose Be verbose. (default=off) Lower the log level setting such that even INFO messages are passed through. 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=`./') --log-level=level Set log level threshold. (default=`2') By default, any log messages are filtered such that only warnings (level 2) or errors (level 3) are printed. This setting allows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information. --log-file[=filename] Print log messages to a file instead of stderr. (default=`RNAs- noop.log') --log-time Include time stamp in log messages. (default=off) --log-call Include file and line of log calling function. (default=off) 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 thresh- old 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 internal 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 cor- rected 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 re- sults. Smaller d leads to larger overlaps between consecutive du- plexes. -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 fea- ture 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 con- flicting 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 calcula- tion for each suboptimal interaction. The -I option should be pre- ferred. (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 algo- rithm originally developed by Rehmsmeier and in parallel by Hofacker. H. Tafer, S. Kehr, J. Hertel, I.L. Hofacker, P.F. Stadler (2009), "RNAs- noop: 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. Su- san, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA sec- ondary 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", Nu- cleic 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 2.7.2 December 2025 RNASNOOP(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS
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