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POFinding the largest open reading frame using Perl
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copied!<p>I've created a program that can read DNA sequences that can generate the complementary strand, which further translates to an mRNA. However, I have to find the longest possible open reading frame for that DNA. I've coded something, but when it prints out the statement, I get no answer. Help?</p> <p>This is what I have;</p> <pre><code># Search for the longest open reading frame for this DNA. print "\nHere is the largest ORF, from 5' to 3':\n" ; local $_ = $RNA_seq ; 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; } </code></pre> <p>Am I missing something?</p>

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