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(vt <v< +LY=c<fkK^w<4&:yI' Yvyy&Y y9XuUuYLvqzuuytZUuwruvtvuuuuvsvuvuo tutxwuwpwxtzxt t tutwtvutuoXuuux vWxuuwxtu|vuuttu tuuvpxvKU= JuJK JvtKRytuuuuuu>tfX@:>4;/[xJ~+KZuIS"YWrf"YWrf"YWf<p<Xk<vn.Xqy~\~tsh~t_f<~f^fz.]~/?5X}}th}<}feglQsue`ztltutG~fgutwh{dYs>vgt~Jt~fgutyf-zXe f!:.|J^$<th^)uX zfz.?-K"~ ~LtFFYtN~;:YtM#,  CU|G~#G!{Gss#!/ud~>.#IvgfX{<#{G&yJ.&YxtYx=]bYZ_a\":>Z_) %s="%s" %s RNAinversehelpdetailed-helpfull-helpversionrepeatalphabetverbosefunctionfinaltempnoTetradanglesnoGUnoClosingGUparamFilenspenergyModelmw2.0.0%s %s %s %s --%s: option `%s' is ambiguous hVR::a:vF:f:T:4d:P:e:%s: invalid option -- %c 1002%s: option unknown: %c%s General Options: Algorithms: Model Details:%s: cannot dump options to stream %s: `--%s' (`-%c') option given more than once%s %s: `--%s' option given more than once%s %s: invalid numeric value: %s %s: cannot open file for writing: %s %s: option `--%s' doesn't allow an argument %s: option `%c%s' doesn't allow an argument %s: option `%s' requires an argument %s: unrecognized option `--%s' %s: option requires an argument -- %c Find RNA sequences with given secondary structureUsage: RNAinverse [OPTIONS]...The program searches for sequences folding into a predefined structure, thereby inverting the folding algorithm. Target structures (in bracket notation) and starting sequences for the search are read alternately from stdin. Characters in the start sequence other than "AUGC" (or the alphabet specified with -a) will be treated as wild cards and replaced by a random character. Any lower case characters in the start sequence will be kept fixed during the search. If necessary, the sequence will be elongated to the length of the structure. Thus a string of "N"s as well as a blank line specify a random start sequence. For each search the best sequence found and its Hamming distance to the start sequence are printed to stdout. If the the search was unsuccessful, a structure distance to the target is appended. The -Fp and -R options can modify the output format, see commandline options below. The program will continue to read new structures and sequences until a line consisting of the single character "@" or an end of file condition is encountered. -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 -R, --repeat[=INT] Search repeatedly for the same structure. (default=`100') If repeats is negative search until -repeats exact solutions are found, no output is done for unsuccessful searches. Be aware, that the program will not terminate if the target structure can not be found. If no value is supplied with this option, the default value is used. -a, --alphabet=ALPHABET Find sequences using only nucleotides from a given alphabet. -v, --verbose In conjunction with a negative value supplied to -R, print the last subsequence and substructure for each unsuccessful search. (default=off) Select additional algorithms which should be included in the calculations. -F, --function=mp Use minimum energy (-Fm), partition function folding (-Fp) or both (-Fmp). (default=`m') In partition function mode, the probability of the target structure exp(-E(S)/kT)/Q is maximized. This probability is written in brackets after the found sequence and Hamming distance. In most cases you'll want to use the -f option in conjunction with -Fp, see below. -f, --final=FLOAT In combination with -Fp stop search when sequence is found with E(s)-F is smaller than final, where F=-kT*ln(Q). -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 -Fp to ensure that both algorithms use the same energy model. --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. References: The calculation of mfe structures is based on dynamic programming algorithm originally developed by M. Zuker and P. Stiegler. The partition function algorithm is based on work by J.S. McCaskill. If you use this program in your work you might want to cite: I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie 125: 167-188 Other useful references are M. Zuker, P. Stiegler (1981) "Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information", Nucl Acid Res 9: 133-148 J.S. McCaskill (1990) "The equilibrium partition function and base pair binding probabilities for RNA secondary structures", Biopolymers 29: 1105-1119 D.H. Turner, N. Sugimoto, S.M. Freier (1988) "RNA structure prediction", Ann Rev Biophys Biophys Chem 17: 167-192 D. Adams (1979) "The hitchhiker's guide to the galaxy", Pan Books, London Written by: Ivo L Hofacker. Report bugs: If in doubt our program is right, nature is at fault. 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