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For a sequence of length n and a base pair span of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short RNA structures. -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 Below are command line options which alter the general behavior of this program -L, --span=INT Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with j-i>span will be allowed. (default=`70') --csv Create comma seperated output (csv) (default=off) 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[=INT] Calculate the partition function and base pairing probability matrix in addition to the mfe structure. (default=`1') Default is calculation of mfe structure only. In addition to the MFE structure we print a coarse representation of the pair probabilities in form of a pseudo bracket notation, followed by the ensemble free energy, as well as the centroid structure derived from the pair probabilities together with its free energy and distance to the ensemble. Finally it prints the frequency of the mfe structure. An additionally passed value to this option changes the behavior of partition function calculation: -p0 Calculate the partition function but not the pair probabilities, saving about 50% in runtime. This prints the ensemble free energy -kT ln(Z). -c, --cutoff=FLOAT Report only base pairs with an average probability > cutoff in the dot plot (default=`0.01') -S, --pfScale=scaling factor In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences. You can also recompile the program to use double precision (see the README file). --mis Output "most informative sequence" instead of simple consensus: For each column of the alignment output the set of nucleotides with frequence greater than average in IUPAC notation. (default=off) -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. -4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (default=off) -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops (default=`2') With -d1 only unpaired bases can participate in at most one dangling end, this is unsupported for the partition function folding. 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 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 interior pairs in a loop of degree 3 and works only for mfe folding. Note that by default (as well as with -d1 and -d3) pf and mfe folding treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same energy model. --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 occur 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) -P, --paramFile=paramfile Read energy parameters from paramfile, instead of using the default parameter set. A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format. --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. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy. -e, --energyModel=INT Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs. --cfactor=DOUBLE Set the weight of the covariance term in the energy function (default=`1.0') --nfactor=DOUBLE Set the penalty for non-compatible sequences in the covariance term of the energy function (default=`1.0') -R, --ribosum_file=ribosumfile use specified Ribosum Matrix instead of normal energy model. Matrixes to use should be 6x6 matrices, the order of the terms is AU, CG, GC, GU, UA, UG. -r, --ribosum_scoring use ribosum scoring matrix. The matrix is chosen according to the minimal and maximal pairwise identities of the sequences in the file. (default=off)Written by: Ivo L Hofacker Report bugs: If in doubt our program is right, nature is at fault. 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