#!/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 amino 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 ] =~ / GC[AGCU] /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 ] =~ / GG[AGCU] /i )             { return G;} # Glycine;
if ( $_ [ 0 ] =~ / CAC|CAU /i )              { return His;} # Histine (start codon);
if ( $_ [ 0 ] =~ / AU[AUC] /i )              { return I;} # Isoleucine;
if ( $_ [ 0 ] =~ / AAA|AAG /i )              { return K;} # Lysine;
if ( $_ [ 0 ] =~ / UUA|UUG|CU[AGCU] /i )     { return Leu;} # Leucine;
if ( $_ [ 0 ] =~ / AUG /i )                  { return M;} # Methionine;
if ( $_ [ 0 ] =~ / AAC|AAU /i )              { return N;} # Asparagine;
if ( $_ [ 0 ] =~ / CC[AGCU] /i )             { return P;} # Proline;
if ( $_ [ 0 ] =~ / CAA|CAG /i )              { return G;} # Glutamine;
if ( $_ [ 0 ] =~ / AGA|AGG|CG[AGCU] /i )     { return R;} # Arginine;
if ( $_ [ 0 ] =~ / AGC|AGU|UC[AGCU] /i )     { return S;} # Serine;
if ( $_ [ 0 ] =~ / AC[AGCU] /i )             { return T;} # Threonine;
if ( $_ [ 0 ] =~ / GU[AGCU] /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;