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RNASNOOP(1) User Commands RNASNOOP(1) NAME RNAsnoop - manual page for RNAsnoop 2.7.0 SYNOPSIS RNAsnoop [options] DESCRIPTION RNAsnoop 2.7.0 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 sec- ondary 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 spe- cial case of H/ACA snoRNA. For general purpose target predictions, please have a look at RNAduplex, RNAup, RNAcofold and RNAplex. Accessi- bility effects can be estimated by RNAsnoop if a RNAplfold accessibil- ity 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 tar- get. 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 accessibil- ity 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 warn- ings (level 2) or errors (level 3) are printed. This setting al- lows 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 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 in- put. (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 recom- puted 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 op- tion). -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 cor- rected 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 con- taining 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 un- paired in spite of constraints. PF folding ignores constraints of type "|". Plotting: Command line options for changing the default behavior of struc- ture layout and pairing probability plots. -I, --produce-ps Draw annotated 2D structures for a list of dot-bracket struc- tures. (default=off) This option allows one to produce interaction figures in PS-for- mat with conservation/accessibility annotation, if available. -N, --direct-redraw Outputs 2D interactions concurrently with the interaction calcu- lation 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 Struc- tures", 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 al- gorithm 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.", Bioinfor- matics: 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 modifica- tion 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 2.7.0 October 2024 RNASNOOP(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS
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