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RNADUPLEX(1) User Commands RNADUPLEX(1) NAME RNAduplex - manual page for RNAduplex 2.7.0 SYNOPSIS RNAduplex [OPTION]... DESCRIPTION RNAduplex 2.7.0 Compute the structure upon hybridization of two RNA strands 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, for the general case use RNAcofold. The computed optimal and suboptimal structure are written to stdout, one structure per line. Each line con- sist 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 -V, --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 -s, --sorted Sort the printed output by free energy. (default=off) --noconv Do not automatically substitute nucleotide "T" with "U". (default=off) --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=`RNAduplex.log') --log-time Include time stamp in log messages. (default=off) --log-call Include file and line of log calling function. (default=off) Algorithms: Select additional algorithms which should be included in the calculations. -e, --deltaEnergy=range Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol). Default is calculation of mfe structure only. 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. The placeholder file name 'DNA' can be used to load DNA parameters 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 -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to he- lices in free ends and multi-loops. (default=`2') With -d1 only unpaired bases can participate in at most one dan- gling end. With -d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the default for mfe and partition function folding (-p). The option -d0 ignores dangling ends altogether (mostly for debugging). With -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two en- closed pairs in a loop of degree 3 and works only for mfe fold- ing. Note that with -d1 and -d3 only the MFE computations will be us- ing this setting while partition function uses -d2 setting, i.e. dangling ends will be treated differently. --noLP Produce structures without lonely pairs (helices of length 1). (default=off) For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally oc- cur as helices of length 1. --noGU Do not allow GU pairs. (default=off) --noClosingGU Do not allow GU pairs at the end of helices. (default=off) --nsp=STRING Allow other pairs in addition to the usual AU,GC,and GU pairs. Its argument is a comma separated list of additionally allowed pairs. If the first character is a "-" then AB will imply that AB and BA are allowed pairs, e.g. --nsp="-GA" will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy. --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. 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 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 Ivo L Hofacker, Ronny Lorenz REPORTING BUGS If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at. SEE ALSO RNAcofold(l) RNAfold(l) RNAduplex 2.7.0 October 2024 RNADUPLEX(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS | SEE ALSO
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