1.4 RNApdist - calculate distances of thermodynamic RNA secondary structures ensembles Stadler, Hofacker, Bonhoeffer Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P, (1993) RNA multistructure landscapes, Euro Biophys J:22,13-24 http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA rnapdist rnapdist perl "RNApdist" 0 seq RNA Sequences File perl " < $value" 1000 8 comparison_options Comparison options 2 compare Which comparisons (-X) perl ($value && $value ne $vdef)? " -X$value" : "" p 2 p p: pairwise (1st/2nd, 3rd/4th etc) m m: distance matrix between all structures f f: each structure to the first one c c: continuously, that is i-th with (i+1)th structure alignment_file Alignment file (-B) perl ($value)? " -B $value" : "" 2 Print an 'alignment' with gaps of the structures, to show matching substructures. The aligned structures are written to file, if specified. Otherwise output is written to stdout, unless the -Xm option is set in which case 'backtrack.file' is used. 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 psfiles *.ps