1.4 RNAheat - calculate specific heat of RNAs Hofacker, 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 J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA rnaheat rnaheat perl "RNAheat" 0 seq RNA Sequences File perl " < $value" 1000 8 control Control options 2 temp_min Lowest temperature, default is 0C (-Tmin) perl (defined $value && $value ne $vdef)? " -Tmin $value" : "" 0 2 temp_max Highest temperature, default is 100C (-Tmax) perl (defined $value && $value ne $vdef)? " -Tmax $value" : "" 100 2 stepsize Calculate partition function every stepsize degrees C. Default is 1C (-h) perl (defined $value && $value ne $vdef)? " -h $value" : "" 1 2 ipoints Produces a smoother curve by increasing ipoints (-m) perl (defined $value && $value ne $vdef)? " -m $value" : "" 2 2 The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve. Default is 2. tetraloops Do not include special stabilizing energies for certain tetraloops (-4) perl ($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") && ($dangling = "") && 0) input Input parameters 2 noGU Do not allow GU pairs (-noGU) perl ($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