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RNAPLEX(1) User Commands RNAPLEX(1) NAME RNAplex - manual page for RNAplex 2.7.0 SYNOPSIS RNAplex [options] DESCRIPTION RNAplex 2.7.0 Find targets of a query RNA reads two RNA sequences from stdin or <filename> and computes optimal and suboptimal secondary structures for their hybridization. The calcu- lation is simplified by allowing only inter-molecular base pairs. Ac- cessibility effects can be estimated by RNAplex if a RNAplfold accessi- bility profile is provided. The computed optimal and suboptimal struc- ture 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 range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. The format is especially useful for computing the hybrid structure between a small probe sequence and a long target sequence. -h, --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 --version Print version and exit -v, --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 -q, --query=STRING File containing the query sequence. Input sequences can be given piped to RNAplex or given in a query file with the -q option. Note that the -q option implies that the -t option is also used -t, --target=STRING File containing the target sequence. Input sequences can be given piped to RNAplex or given in a tar- get file with the -t option. Note that the -t option implies that the -q option is also used -a, --accessibility-dir=STRING Location of the accessibility profiles. This option switches the accessibility modes on and indicates in which directory accessibility profiles as generated by RNAplfold can be found -b, --binary Allow the reading and parsing of memory dumped opening energy file (default=off) The -b option allows one to read and process opening energy files which are saved in binary format This can reduce by a factor of 500x-1000x the time needed to process those files. RNAplex recognizes the corresponding opening energy files by looking for files named after the sequence and containing the suffix _openen_bin. Please look at the man page of RNAplfold if you need more information on how to produce binary opening en- ergy files. --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. (de- fault=`RNAplex.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. -l, --interaction-length=INT Maximal length of an interaction (default=`40') Maximal allowed length of an interaction -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 (-a option) -p, --probe-mode Compute Tm for probes (default=off) Use this option if you want to compute the melting temperature of your probes -Q, --probe-concentration=DOUBLE Set the probe concentration for the Tm computation (default=`0.1') -N, --na-concentration=DOUBLE Set the Na+ concentration for the Tm computation. (default=`1.0') -M, --mg-concentration=DOUBLE Set the Mg2+ concentration for the Tm computation. (default=`1.0') -K, --k-concentration=DOUBLE Set the K+ concentration for the Tm computation. (default=`1.0') -U, --tris-concentration=DOUBLE Set the tris+ concentration for the Tm computation. (default=`1.0') -f, --fast-folding=INT Speedup of the target search (default=`0') This option allows one to decide if the backtracking has to be done (-f 0, -f 2) or not (-f 1). For -f 0 the structure is com- puted based on the standard energy model. This is the slowest and most precise mode of RNAplex. With -f 2, the structure is computed based on the approximated plex model. If a lot of tar- gets are returned this is can greatly improve the runtime of RNAplex. -f 1 is the fastest mode, as no structure are recom- puted -V, --scale-accessibility=DOUBLE Rescale all opening energy by a factor V (default=`1.0') Scale-factor for the accessibility. If V is set to 1 then the scaling has no effect on the accessibility. -A, --alignment-mode Tells RNAplex to compute interactions based on alignments (default=off) If the A option is set RNAplex expects clustalw files as input for the -q and -t option. -k, --convert-to-bin If set, RNAplex will convert all opening energy file in a direc- tory set by the -a option into binary opening energy files (default=off) RNAplex can be used to convert existing text formatted opening energy files into binary formatted files. In this mode RNAplex does not compute interactions. -z, --duplex-distance=INT Distance between target 3' ends of two consecutive duplexes (default=`0') Distance between the target 3'ends of two consecutive duplexes. Should be set to the maximal length of interaction to get good results Smaller z leads to larger overlaps between consecutive duplexes. -e, --energy-threshold=DOUBLE Minimal energy for a duplex to be re- turned (default=`-100000') Energy threshold for a duplex to be returned. The threshold is set on the total energy of interaction, i.e. the hybridization energy corrected for opening energy if -a is set or the energy corrected by -c. If unset, only the mfe will be returned -L, --WindowLength=INT Tells how large the region around the target site should be for redrawing the alignment interaction (default=`1') This option allows one to specify how large the region surround- ing the target site should be set when generating the alignment figure of the interaction Structure Constraints: Command line options to interact with the structure constraints feature of this program -C, --constraint Calculate structures subject to constraints. (default=off) The program reads first the sequence, then a string containing constraints on the structure for the query sequence encoded with the symbols: . (no constraint for this base) | (the correspond- ing base has to be paired) Energy Parameters: Energy parameter sets can be adapted or loaded from user-pro- vided input files -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. (default=`37.0') -P, --paramFile=paramfile Read energy parameters from paramfile, instead of using the de- fault parameter set. Different sets of energy parameters for RNA and DNA should ac- company your distribution. See the RNAlib documentation for de- tails on the file format. When passing the placeholder file name "DNA", DNA parameters are loaded without the need to actually specify any input file. -4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. (default=off) Mostly for testing. --salt=DOUBLE Set salt concentration in molar (M). Default is 1.021M. --saltInit=DOUBLE Provide salt correction for duplex initialization (in kcal/mol). Model Details: Tweak the energy model and pairing rules additionally using the following parameters --helical-rise=FLOAT Set the helical rise of the helix in units of Angstrom. (default=`2.8') Use with caution! This value will be re-set automatically to 3.4 in case DNA parameters are loaded via -P DNA and no further value is provided. --backbone-length=FLOAT Set the average backbone length for looped regions in units of Angstrom. (default=`6.0') Use with caution! This value will be re-set automatically to 6.76 in case DNA parameters are loaded via -P DNA and no further value is provided. Plotting: Command line options for changing the default behavior of struc- ture layout and pairing probability plots -I, --produce-ps=STRING Draw an alignment annotated interaction from RNAplex. This option allows one to produce interaction figures in PS-for- mat a la RNAalifold, where base-pair conservation is represented in color-coded format. In this mode no interaction are computed, but the -I option indicates the location of the file containing interactions between two RNA (alignments/sequence) from a previ- ous run. If the -A option is not set a structure figure a la RNAfold with color-coded annotation of the accessibilities is returned 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 and I.L. Hofacker (2008), "RNAplex: a fast tool for RNA-RNA interaction search.", Bioinformatics: 24(22), pp 2657-2663 S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster (1993), "RNA multi-structure landscapes", Euro Biophys J: 22, pp 13-24 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. RNAplex 2.7.0 October 2024 RNAPLEX(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS
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