Hello World Examples
Using the flat interface
MFE prediction
use RNA; # The RNA sequence my $seq = "GAGUAGUGGAACCAGGCUAUGUUUGUGACUCGCAGACUAACA"; # compute minimum free energy (MFE) and corresponding structure my ($ss, $mfe) = RNA::fold($seq); # print output printf "%s\n%s [ %6.2f ]\n", $seq, $ss, $mfe;
Using the object oriented interface
MFE prediction
#!/usr/bin/perl use warnings; use strict; use RNA; my $seq1 = "CGCAGGGAUACCCGCG"; # create new fold_compound object my $fc = new RNA::fold_compound($seq1); # compute minimum free energy (mfe) and corresponding structure my ($ss, $mfe) = $fc->mfe(); # print output printf "%s [ %6.2f ]\n", $ss, $mfe;
Changing the Model Settings
Using the flat interface
MFE prediction at different temperature and dangle model
use RNA; # The RNA sequence my $seq = "GAGUAGUGGAACCAGGCUAUGUUUGUGACUCGCAGACUAACA"; # create a new model details structure my $md = new RNA::md(); # change temperature and dangle model $md->{temperature} = 20.0; # 20 Deg Celcius $md->{dangles} = 1; # Dangle Model 1 # create a fold compound my $fc = new RNA::fold_compound($seq, $md); # predict Minmum Free Energy and corresponding secondary structure my ($ss, $mfe) = $fc->mfe(); # print sequence, structure and MFE printf "%s\n%s [ %6.2f ]\n", $seq, $ss, $mfe;
Using the object oriented interface
MFE prediction at different temperature and dangle model