#!/usr/bin/perl -w $sequence1='file1.txt'; 
 open(SEQUENCE,$sequence1); 
 $seq=<SEQUENCE>; 
 print $seq, "\n"; 
 $RNA=$seq; $RNA=~s/T/U/g; 
 print "\n here is mRNA $RNA \n"; 
 close SEQUENCE; 
 $rna1=$RNA; 
 print "\n Here is the 1st frame $rna1 \n" ; 
 $rna2=substr($RNA,1) ; 
 print " Here is the 2nd frame $rna2 \n"; 
 $rna3=substr($RNA,2) ; 
 print "Here is the 3rd frame $rna3 \n"; 
 $length1= length$rna1; 
 $length2= length$rna2; 
 $length3= length$rna3; 
 print "1st line ORFs\n"; 
 for ($i = 0; $i <= ($length1 - 3); $i = $i + 3)
  { $codon1 = substr($rna1, $i, 3); 
  print $codon1," "; 
  }
 print "2nd line ORFs\n"; 
 for ($i = 0; $i <= ($length2 - 3); $i = $i + 3) 
 { $codon2 = substr($rna2, $i, 3); 
 print $codon2," "; 
 } 
 print "\n 3rd line ORFs\n";
 for ($i = 0; $i <= ($length3 - 3); $i = $i + 3) 
 { $codon3 = substr($rna3, $i, 3); 
 print $codon3," "; 
 } 
 local $_ = $RNA ; 
 while ( / AUG /g ) 
 { my $start = pos () - 2 ;
  if ( / UGA|UAA|UAG /g ) 
  { my $stop = pos ;
   $gene = substr ( $_ , $start - 1 , $stop - $start + 1 ), $/ ; 
   print "$gene" ; 
   } 
 # The next set of commands translates the ORF found above for an amin
+o acid seq. 
 print "\nThe largest reading Frame is:\t\t\t" . $protein { "gene" } .
+ "\n" ; 
 
 sub translate { 
  my ( $gene , $reading_frame ) = @_ ; 
  my %protein = (); 
  for ( $i = $reading_frame ; $i < length ( $gene ); $i += 3 ) 
  { $codon = substr ( $gene , $i , 3 ); 
  $amino_acid = translate_codon( $codon ); 
  $protein { $amino_acid }++; 
  $protein { "gene" } .= $amino_acid ; 
  } 
  return %protein ; 
  } 
  
  sub translate_codon { 
   if ( $_ 0 =~ / GCAGCU /i ) { return A;} # Alanine;
   if ( $_ 0 =~ / UGC|UGU /i ) { return C;} # Cysteine 
   if ( $_ 0 =~ / GAC|GAU /i ) { return D;} # Aspartic Acid; 
   if ( $_ 0 =~ / GAA|GAG /i ) { return Q;} # Glutamine; 
   if ( $_ 0 =~ / UUC|UUU /i ) { return F;} # Phenylalanine; 
   if ( $_ 0 =~ / GGAGCU /i ) { return G;} # Glycine; 
   if ( $_ 0 =~ / CAC|CAU /i ) { return His;} # Histine (start codon);
+ 
   if ( $_ 0 =~ / AUAUC /i ) { return I;} # Isoleucine; 
   if ( $_ 0 =~ / AAA|AAG /i ) { return K;} # Lysine; 
   if ( $_ 0 =~ / UUA|UUG|CUAGCU /i ) { return Leu;} # Leucine; 
   if ( $_ 0 =~ / AUG /i ) { return M;} # Methionine; 
   if ( $_ 0 =~ / AAC|AAU /i ) { return N;} # Asparagine; 
   if ( $_ 0 =~ / CCAGCU /i ) { return P;} # Proline; 
   if ( $_ 0 =~ / CAA|CAG /i ) { return G;} # Glutamine; 
   if ( $_ 0 =~ / AGA|AGG|CGAGCU /i ) { return R;} # Arginine; 
   if ( $_ 0 =~ / AGC|AGU|UCAGCU /i ) { return S;} # Serine; 
   if ( $_ 0 =~ / ACAGCU /i ) { return T;} # Threonine; 
   if ( $_ 0 =~ / GUAGCU /i ) { return V;} # Valine; 
   if ( $_ 0 =~ / UGG /i ) { return W;} # Tryptophan; 
   if ( $_ 0 =~ / UAC|UAU /i ) { return Y;} # Tyrosine; 
   if ( $_ 0 =~ / UAA|UGA|UAG /i ) { return "***" ;} # Stop Codons;
    } 
    } 
    exit;
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