VIENNARNA 1.4 RNAeval - calculate energy of RNA sequences on given secondary structure 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 http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA rnaeval rnaeval perl "RNAeval" rnaeval 0 seqstruct Sequences/Structures File (output of RNAfold) perl " < $value" 1000 rnafold_struct perl 1 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 Don't give stabilizing energies to single stacked bases in dangling ends (-d) perl ($value)? " -d" : "" 0 2 Do not give stabilizing energies to unpaired bases adjacent to helices in multiloops and free ends ('dangling ends'). Same as -d0, opposite of -d1 (the default). d2 Treat dangling ends as in the partition function algorithm (-d2) perl ($value)? " -d2" : "" 0 2 Treat dangling ends as in the partition function algorithm, i.e. bases adjacent to helices in multiloops and free ends give a stabilizing energy contribution, regardless whether they're paired or unpaired. logML Let multiloop energies depend logarithmically on the size (-logML) perl ($value)? " -logML" : "" 0 2 Let multiloop energies depend logarithmically on the size, instead of the usual linear energy function. parameter Parameter file (-P) perl ($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