In PERL programing, RNA sequence is converted into protein sequence by substituting equivalent amino acid characters to triplet characters of RNA. This method is followed to find six reading frame (three in forward direction, and three in reverse direction). In this program, I have used associative array (also known as hash array) to associate triplet characters with amino acid character.

The associate array corresponding to codon table is arranged to 20 amino acid character. The triplet codon table is shown bellow:

Triplet Codon Table


Source Code:

print “Enter the RNA sequence: “;
$rna = <>;
chomp($rna);
$rna =~s/[^acgu]//ig;
my $rna = uc($rna);
my(%genetic_code) = (
‘UCA’ => ‘S’, # Serine
‘UCC’ => ‘S’, # Serine
‘UCG’ => ‘S’, # Serine
‘UCU’ => ‘S’, # Serine
‘UUC’ => ‘F’, # Phenylalanine
‘UUU’ => ‘F’, # Phenylalanine
‘UUA’ => ‘L’, # Leucine
‘UUG’ => ‘L’, # Leucine
‘UAC’ => ‘Y’, # Tyrosine
‘UAU’ => ‘Y’, # Tyrosine
‘UAA’ => ‘_’, # Stop
‘UAG’ => ‘_’, # Stop
‘UGC’ => ‘C’, # Cysteine
‘UGU’ => ‘C’, # Cysteine
‘UGA’ => ‘_’, # Stop
‘UGG’ => ‘W’, # Tryptophan
‘CUA’ => ‘L’, # Leucine
‘CUC’ => ‘L’, # Leucine
‘CUG’ => ‘L’, # Leucine
‘CUU’ => ‘L’, # Leucine
‘CCA’ => ‘P’, # Proline
‘CAU’ => ‘H’, # Histidine
‘CAA’ => ‘Q’, # Glutamine
‘CAG’ => ‘Q’, # Glutamine
‘CGA’ => ‘R’, # Arginine
‘CGC’ => ‘R’, # Arginine
‘CGG’ => ‘R’, # Arginine
‘CGU’ => ‘R’, # Arginine
‘AUA’ => ‘I’, # Isoleucine
‘AUC’ => ‘I’, # Isoleucine
‘AUU’ => ‘I’, # Isoleucine
‘AUG’ => ‘M’, # Methionine
‘ACA’ => ‘T’, # Threonine
‘ACC’ => ‘T’, # Threonine
‘ACG’ => ‘T’, # Threonine
‘ACU’ => ‘T’, # Threonine
‘AAC’ => ‘N’, # Asparagine
‘AAU’ => ‘N’, # Asparagine
‘AAA’ => ‘K’, # Lysine
‘AAG’ => ‘K’, # Lysine
‘AGC’ => ‘S’, # Serine
‘AGU’ => ‘S’, # Serine
‘AGA’ => ‘R’, # Arginine
‘AGG’ => ‘R’, # Arginine
‘CCC’ => ‘P’, # Proline
‘CCG’ => ‘P’, # Proline
‘CCU’ => ‘P’, # Proline
‘CAC’ => ‘H’, # Histidine
‘GUA’ => ‘V’, # Valine
‘GUC’ => ‘V’, # Valine
‘GUG’ => ‘V’, # Valine
‘GUU’ => ‘V’, # Valine
‘GCA’ => ‘A’, # Alanine
‘GCC’ => ‘A’, # Alanine
‘GCG’ => ‘A’, # Alanine
‘GCU’ => ‘A’, # Alanine
‘GAC’ => ‘D’, # Aspartic Acid
‘GAU’ => ‘D’, # Aspartic Acid
‘GAA’ => ‘E’, # Glutamic Acid
‘GAG’ => ‘E’, # Glutamic Acid
‘GGA’ => ‘G’, # Glycine
‘GGC’ => ‘G’, # Glycine
‘GGG’ => ‘G’, # Glycine
‘GGU’ => ‘G’  # Glycine
);
my ($protein) = “”;
for(my $i=0;$i<length($rna)-2;$i+=3)
{
$codon = substr($rna,$i,3);
$protein .= $genetic_code{$codon};
}
print “Translated protein sequence is $protein”;
<>;

This program can also used for six reading frame, by changing the three character shift in forward and reverse of the RNA sequence.