--- a/miRDeep_plant.pl	Thu Oct 30 21:29:35 2014 -0400
+++ b/miRDeep_plant.pl	Thu Nov 13 22:43:35 2014 -0500
@@ -3,7 +3,7 @@
 use warnings;
 use strict;
 use Getopt::Std;
-use RNA;
+#use RNA;
 
 
 ################################# MIRDEEP #################################################
@@ -385,14 +385,26 @@
 	my $cpt_ega = 1;
 	
 	my ($seq,$number_of_randomizations)=@_;
-	my $str =$seq;
-	my $mfe = RNA::fold($seq,$str);
+	#my $str =$seq;
+	#my $mfe = RNA::fold($seq,$str);
+		my $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`;
+		my @rawfolds=split/\s+/,$rnafold;
+		my $str=$rawfolds[1];
+		my $mfe=$rawfolds[-1];
+		$mfe=~s/\(//;
+		$mfe=~s/\)//;
 
 	for (my $i=0;$i<$number_of_randomizations;$i++) {
 		$seq = shuffle_sequence_dinucleotide($seq);
-		$str = $seq;
+		#$str = $seq;
 	
-		my $rand_mfe = RNA::fold($str,$str);
+		#my $rand_mfe = RNA::fold($str,$str);
+		$rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`;
+		my @rawfolds=split/\s+/,$rnafold;
+		my $str=$rawfolds[1];
+		my $rand_mfe=$rawfolds[-1];
+		$rand_mfe=~s/\(//;
+		$rand_mfe=~s/\)//;
 	
 		if ($rand_mfe < $mfe) {
 			$cpt_inf++;