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(v <v< 9LY=c<fkבKt^w<4#:y<I' Yvyy&Y z9X@:>4;/[xJ~+KZuIS"YWrf"YWrf"YWfYs>tgt~Jt~fgutyf-yXe f!:.#|J^%<tؑ^)=;u zfz.N!I"~ B~QDYt KMY'tG$_ X X;\{N~G[|Dss#!/u~>.#>:IvegfsguL<\ZG{D(# J&. XC{S)&GYxtYx =]bYZ_a\":>Z_) %s="%s" %s RNAfoldhelpdetailed-helpfull-helpversionconstraintnoconvnoPSpartfuncMEApfScalecirctempnoTetradanglesnoLPnoGUnoClosingGUparamFilenspenergyModelw2.0.0%s %s %s %s --%s: option `%s' is ambiguous hVCp::S:cT:4d:P:e:%s: invalid option -- %c 121.%s: option unknown: %c%s Usage: RNAfold [OPTIONS]... 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 Calculate minimum free energy secondary structures and partition function of RNAsThe program reads RNA sequences from stdin, calculates their minimum free energy (mfe) structure and prints to stdout the mfe structure in bracket notation and its free energy. If the -p option was given it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout. It also produces PostScript files with plots of the resulting secondary structure graph and a "dot plot" of the base pairing matrix. The dot plot shows a matrix of squares with area proportional to the pairing probability in the upper right half, and one square for each pair in the minimum free energy structure in the lower left half. For each pair i-j with probability p>10E-6 there is a line of the form i j sqrt(p) ubox in the PostScript file, so that the pair probabilities can be easily extracted. Sequences may be provided in a simple text format where each sequence occupies a single line. Output files are named "rna.ps" and "dot.ps". Existing files of the same name will be overwritten. It is also possible to provide sequence data in FASTA format. In this case, the first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively. Once FASTA input was provided all following sequences must be in FASTA format too. The program will continue to read new 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 -C, --constraint Calculate structures subject to constraints. (default=off) The program reads first the sequence, then a string containing constraints on the structure encoded with the symbols: . (no constraint for this base) | (the corresponding base has to be paired x (the base is unpaired) < (base i is paired with a base j>i) > (base i is paired with a base jSST S) %!SV*VVVyV>VVT V) %!V{%!{*\\*\\\y\>\\T \) %!\^~{^^{^^^Py^^P>^A^w^Z^ZqPq^&^T ^) ^ P !^ !!P!%!^8BU05UaV^V^^^V^y^>]V]^AGVGw^V^ ) ^ *Xd}XT~XX:XXXXXOX X4XXX'XwXXRX&HX|[]m]|]]]]]26]w]T]|%!|0!1!w1!8!w8!!w00!`!U0!`!T0!`!Q`!j!Sk!!S0!C!R0!F!X0!`!Yc!i!Pk!u!P!!U!!T!!Q!!w!!w!!U!!T!!Q!!S!!S!!R!!P!!P RNAfold_cmdline_parser_init RNAfold_cmdline_parser_params_init RNAfold_cmdline_parser_required6 RNAfold_cmdline_parser_dump RNAfold_cmdline_parser_free 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