Bio::Tools::CodonTable 1.4

Bio::Tools::CodonTable is a bioperl codon table object.

SYNOPSIS

# This is a read-only class for all known codon tables. The IDs are
# the ones used by nucleotide sequence databases. All common IUPAC
# ambiguity codes for DNA, RNA and animo acids are recognized.

# to use
use Bio::Tools::CodonTable;

# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
$myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 3 );

# change codon table
$myCodonTable->id(5);

# examine codon table
print join ( , "The name of the codon table no.", $myCodonTable->id(4),
"is:", $myCodonTable->name(), "n");

# translate a codon
$aa = $myCodonTable->translate(ACU);
$aa = $myCodonTable->translate(act);
$aa = $myCodonTable->translate(ytr);

# reverse translate an amino acid
@codons = $myCodonTable->revtranslate(A);
@codons = $myCodonTable->revtranslate(Ser);
@codons = $myCodonTable->revtranslate(Glx);
@codons = $myCodonTable->revtranslate(cYS, rna);

#boolean tests
print "Is a startn" if $myCodonTable->is_start_codon(ATG);
print "Is a termianatorn" if $myCodonTable->is_ter_codon(tar);
print "Is a unknownn" if $myCodonTable->is_unknown_codon(JTG);

Codon tables are also called translation tables or genetics codes since that is what they try to represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups presented at the NCBI Genetic Codes Home page.

CodonTable is a BioPerl class that knows all current translation tables that are used by primary nucleotide sequence databases (GenBank, EMBL and DDBJ). It provides methods to output information about tables and relationships between codons and amino acids.

This class and its methods recognized all common IUPAC ambiguity codes for DNA, RNA and animo acids. The translation method follows the conventions in EMBL and TREMBL databases.
It is a nuisance to separate RNA and cDNA representations of nucleic acid transcripts. The CodonTable object accepts codons of both type as input and allows the user to set the mode for output when reverse translating. Its default for output is DNA.

Note: This class deals primarily with individual codons and amino acids. However in the interest of speed you can translate longer sequence, too. The full complexity of protein translation is tackled by Bio::PrimarySeqI::translate.