1.4 RNAinverse - find RNA sequences with given secondary structure Hofacker 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 rnainverse rnainverse perl "RNAinverse" rnainverse 0 seqstruct Sequences/Structures File perl " < $value" 1000 Target structures and starting sequences for the search are read alternately from stdin. If a '0' is given instead of a starting sequence a random sequence is used. control Control options 2 folding Folding method (-F) perl (defined $value && $value ne $vdef)? " -F$value" : "" m 2 m m: minimum energy p p: partition function mp mp: both final Stop search when sequence is found with E(s)-F smaller than this value (-f) perl (defined $value)? " -f $value" : "" 2 In combination with -Fp F=-kT*ln(Q) perl $folding =~ /p/ repeats Search repeatedly for the same structure (-R) perl (defined $value)? " -R $value" : "" 2 If '0' was given instead of a starting sequence, a new random starting sequences is used for each subsequent trial. If repeats is negative search until -repeats exact solutions are found, no output is done for unsuccessful searches. The program will not terminate if the target can not be found. alphabet Find sequences using only bases from this alphabet (-a) perl ($value)? " -a $value" : "" 2 others_options Other options 2 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 only unpaired bases can participate in at most one dangling end -d -d: ignores dangling ends altogether -d2 -d2: the check is ignored, this is the default for partition function folding. 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") && ($dangling = "") && 0) noGU Do not allow GU pairs (-noGU) perl ($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 1: use energy parameters for GC pairs 2 2: use energy parameters for AU pairs 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