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Conversion Codons -> Amino Acids -> Protein
Data Munging example from a Well House Consultants training course
More on Data Munging [link]

This example is described in the following article(s):
   • Converting codons via Amino Acids to Proteins in Perl - [link]

This example references the following resources:

Source code: bacon Module: P669
# Homo sapiens cyclin-dependent kinase 5, regulatory subunit 2 (p39) (CDK5R2), mRNA
# from http://www.ncbi.nlm.nih.gov/nuccore/384551662?report=fasta

open(FH,"cdk.fasta") or die;
$debug = 0; # Set to 1 for longer output

# Slurp the whole data file into a string
@cdk = grep(/^[^#]/,<FH>);
$cdk = join("",@cdk);
if ($debug) { print $cdk,"\n"; }

$cdk =~ s/\n//g;
if ($debug) { print $cdk,"\n"; }

# Quick (but hard to maintain) development trick - write code for a sub
# near where it is called

sub getconversion {
        # Create has to covert groups of 3 codons to amino acids
        # Data is stored at the end of this program
        while (<DATA>) {
                s/,//g; # Data includes some unwanted commas - strip them
                my ($fullname, $code, @tripples) = split;
                foreach my $three (@tripples) {
                        $amino_code{$three} = $code;
                } # $fullname never actually used - available for future!


if ($debug) {
        foreach $trip (keys %amino_code) {
                print "$trip $amino_code{$trip}\n";

$report = "";

# Convert groups of 3 codons into amino acids and assemble into proteins

while ($cdk =~ /[ACGT]{3}/g) { # groups of 3 codons
        $acid = $amino_code{$&};
        if ($debug) {
                print "$& - $acid\n";
        if ($acid eq "Stop") {
                $report .= "\n\n";
        } else {
                $report .= $acid;

print "$report\n";

Isoleucine I ATT, ATC, ATA
Phenylalanine F TTT, TTC
Methionine M ATG
Cysteine C TGT, TGC
Alanine A GCT, GCC, GCA, GCG
Glycine G GGT, GGC, GGA, GGG
Proline P CCT, CCC, CCA, CCG
Threonine T ACT, ACC, ACA, ACG
Tyrosine Y TAT, TAC
Tryptophan W TGG
Glutamine Q CAA, CAG
Asparagine N AAT, AAC
Histidine H CAT, CAC
Glutamic_acid E GAA, GAG
Aspartic_acid D GAT, GAC
Lysine K AAA, AAG
Stop_codons Stop TAA, TAG, TGA

Learn about this subject
This module and example are covered on our public Perl for Larger Projects course. If you have a group of three or more trainees who need to learn the subject, we can also arrange a private or on site course for you.

Books covering this topic
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Other Examples
This example comes from our "Data Munging" training module. You'll find a description of the topic and some other closely related examples on the "Data Munging" module index page.

Full description of the source code
You can learn more about this example on the training courses listed on this page, on which you'll be given a full set of training notes.

Many other training modules are available for download (for limited use) from our download centre under an Open Training Notes License.

Other resources
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This is a sample program, class demonstration or answer from a training course. It's main purpose is to provide an after-course service to customers who have attended our public private or on site courses, but the examples are made generally available under conditions described below.

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