1.4 RNAsubopt - calculate suboptimal secondary structures of RNAs Wuchty, Hofacker, Fontana S. Wuchty, W. Fontana, I. L. Hofacker and P. Schuster Complete Suboptimal Folding of RNA and the Stability of Secondary Structures, Biopolymers, 49, 145-165 (1999) http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA rnasubopt rnasubopt perl "RNAsubopt" rnasubopt 0 seq RNA Sequences File perl " < $value" 1000 8 control Control 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 mfe Calculate suboptimal structures within this range kcal/mol of the mfe (-e) perl (defined $value && $value != $vdef)? " -e $value" : "" 1 2 lodos Calculate the Lower Density of States (-lodos) perl ($value)? " -lodos" : "" 0 2 Output lines consist of an energy followed by the number of structures with that energy, suitable for plotting the density of states. Does not print the structures themseleves. 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") && ($dangling = "") && 0) logML Recalculate energies of structures using a logarithmic energy function for multi-loops (-logML) perl ($value)? " -logML" : "" 0 2 This option does not effect structure generation, only the energies that is printed out. Since logML lowers energies somewhat, some structures may be missing. ep Only print structures with energy within this prange of the mfe (with -logML) (-ep) perl (defined $value)? " -ep $value" : "" 2 perl $logML sort Sort the structures by energy (-sort) perl ($value)? " -sort" : "" 0 2 input Input parameters 2 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. 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 psfiles *.ps