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RNA2DFOLD(1) User Commands RNA2DFOLD(1) NAME RNA2Dfold - manual page for RNA2Dfold 2.7.0 SYNOPSIS RNA2Dfold [OPTION]... DESCRIPTION RNA2Dfold 2.7.0 Compute MFE structure, partition function and representative sample structures of k,l neighborhoods The program partitions the secondary structure space into (base- pair)distance classes according to two fixed reference structures. It expects a sequence and two secondary structures in dot-bracket notation as its inputs. For each distance class, the MFE representative, Boltz- mann probabilities and Gibbs free energy is computed. Additionally, a stochastic backtracking routine allows one to produce samples of repre- sentative suboptimal secondary structures from each partition -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 -j, --numThreads=INT Set the number of threads used for calculations (only available when compiled with OpenMP support) --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=`RNA2Dfold.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. The Minimum free energy (MFE) and a structure representative are calculated in any case. -p, --partfunc calculate partition function and thus, Boltzmann probabilities and Gibbs free energy (default=off) --stochBT=INT backtrack a certain number of Boltzmann samples from the appro- priate k,l neighborhood(s) --neighborhood=<k>:<l> backtrack structures from certain k,l-neighborhood only, can be specified multiple times (<k>:<l>,<m>:<n>,...) -K, --maxDist1=INT maximum distance to first reference structure If this value is set all structures that exhibit a basepair dis- tance greater than maxDist1 will be thrown into a distance class denoted by K=L=-1 -L, --maxDist2=INT maximum distance to second reference structure If this value is set all structures that exhibit a basepair dis- tance greater than maxDist1 will be thrown into a distance class denoted by K=L=-1 -S, --pfScale=DOUBLE In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). (default=`1.07') The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences. --noBT do not backtrack structures, calculate energy contributions only (default=off) -c, --circ Assume a circular (instead of linear) RNA molecule. (default=off) 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. 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 (possible values="0", "2" default=`2') With -d2 dangling energies will be added for the bases adjacent to a helix on both sides in any case. The option -d0 ignores dangling ends altogether (mostly for debugging). --noGU Do not allow GU pairs. (default=off) --noClosingGU Do not allow GU pairs at the end of helices. (default=off) --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 R. Lorenz, C. Flamm, I.L. Hofacker (2009), "2D Projections of RNA fold- ing Landscapes", GI, Lecture Notes in Informatics, German Conference on Bioinformatics 2009: 157, pp 11-20 M. Zuker, P. Stiegler (1981), "Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information", Nucl Acid Res: 9, pp 133-148 J.S. McCaskill (1990), "The equilibrium partition function and base pair binding probabilities for RNA secondary structures", Biopolymers: 29, pp 1105-1119 I.L. Hofacker and P.F. Stadler (2006), "Memory Efficient Folding Algo- rithms for Circular RNA Secondary Structures", Bioinformatics D. Adams (1979), "The hitchhiker's guide to the galaxy", Pan Books, London The calculation of mfe structures is based on dynamic programming algo- rithm originally developed by M. Zuker and P. Stiegler. The partition function algorithm is based on work by J.S. McCaskill. 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 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. RNA2Dfold 2.7.0 October 2024 RNA2DFOLD(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS
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