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

[Richard Adams]

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

e.g.,
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.

Richard



-- 
Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

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