[Bioperl-l] About reverse translation using CodonUsage table ?

Richard Adams Richard.Adams at ed.ac.uk
Fri Sep 24 04:20:23 EDT 2004

You  can use Bio::Tools::CodonTable::revtranslate to reverse translate

use Bio::Tools::CodonTable;
my $seq  = 'DFGTR';

#get your codon table of choice
my $CodonTable2  = Bio::Tools::CodonTable -> new ( -id => 3 );
my @dna_seq; 
my @seq = split '', $seq;
for my $aa (@seq) {

	my @codons = $codonTable2->revtranslate($aa);
	push @dna_seq, \@codons;

## now you have an array of arrays where each sequence position has a reference
to a list of possible codons.
I don't think there's a way to translate alternative codons back to IUPAC ids at the moment,
it would  be worth doing. I'll look into it.


Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK

Tel: 44 131 651 1084
richard.adams at ed.ac.uk

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