VIENNARNA 1.4 RNAfold - calculate secondary structures of RNAs Hofacker, Fontana, Bonhoeffer, Stadler 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 A. Walter, D Turner, J Kim, M Lyttle, P Muller, D Mathews, M Zuker Coaxial stacking of helices enhances binding of oligoribonucleotides. PNAS, 91, pp 9218-9222, 1994 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: 11051119 D.H. Turner N. Sugimoto and 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 http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA rnafold rnafold perl "RNAfold" rnafold 0 seq RNA Sequences File perl " < $value" 1000 8 control Control options 2 partition Calculate the partition function and base pairing probability matrix (-p) perl ($value)? " -p" : "" 0 2 pf Calculate the pf without pairing matrix (-p0) perl ($value)? " -p0" : "" 0 2 Calculate the pf without pairing matrix and print the ensemble free energy -kT ln(Z). This is much faster. temperature Rescale energy parameters to a temperature of temp C. (-T) perl (defined $value && $value ne $vdef)? " -T $value" : "" 37 2 tetraloops Do not include special stabilizing energies for certain tetraloops (-4) perl ($value)? " -4" : "" 0 2 dangling How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d) perl ($value)? " $value" : "" "" 2 -d -d2 How to treat 'dangling end' energies for bases adjacent to helices in free ends and multiloops: Normally only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, this is the default for partition function folding (-p). -d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model. The -d2 options is available for RNAfold, RNAeval, and RNAinverse only. no message perl (! (defined $rnafold || defined $rnaeval || defined $rnainverse) && ($dangling eq "-d2") && ($dangling = "") && 0) scale Use scale*mfe as an estimate for the free energy (-S) perl ($value)? " -S $value" : "" 2 In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, usefull values are 1.0 to 1.2. Occasionally needed for long sequences. You can also recompile the programm to use double precision (see the README file). input Input parameters 2 constraints Calculate structures subject to constraints (-C) perl ($value)? " -C" : "" 0 2 The programm reads first the sequence then the a string containg constraints on the structure encoded with the symbols: | (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 j<i) matching brackets ( ) (base i pairs base j) Pf folding ignores constraints of type '|' '<' and '>', but disallow all pairs conflicting with a constraint of type 'x' or '( )'. This is usually sufficient to enforce the constraint. noLP Avoid lonely pairs (helices of length 1) (-noLP) perl ($value)? " -noLP" : "" 0 2 This works by disallowing pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1. noGU Do not allow GU pairs (-noGU) perl ($value)? " -noGU" : "" 0 2 noCloseGU Do not allow GU pairs at the end of helices (-noCloseGU) perl ($value)? " -noCloseGU" : "" 0 2 nsp Non standard pairs (comma seperated list) (-nsp) perl ($value)? " -nsp $value" : "" 2 Allow other pairs in addition to the usual AU,GC,and GU pairs. pairs is a comma seperated list of additionally allowed pairs. If a the first character is a '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy. parameter Parameter file (-P) perl ($value)? " -P $value" : "" 2 Read energy parameters from paramfile, instead of using the default parameter set. A sample parameterfile should accompany your distribution. See the RNAlib documentation for details on the file format. energy Energy parameters for the artificial ABCD... alphabet (-e) perl ($value)? " -e $value" : "" 2 1 2 output_options Output options outfile Result file perl ($value)? " > $value" : "" struct.out 2000 rnafold_struct perl ! $partition b2ct converts the bracket notation produced by RNAfold into an .ct file, as produced by Zukers mfold perl ($value)? " ; head -2 rnafold.out | b2ct > rnafold.ct " : "" 0 2000 readseq perl "/local/gensoft/lib/ViennaRNA/readseq -f=19 -a $seq > $seq.tmp && (cp $seq $seq.orig && mv $seq.tmp $seq) ; " -10 perl defined $rnafold || defined $rnasubopt ctfiles perl $b2ct rnafold.ct psfiles *.ps