[Biopython-dev] [Bug 2547] Translation of ambiguous codons like NNN and TAN

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2547





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-21 11:25 EST -------
I've managed to cobble together my first ever Perl program from scratch, and
established that BioPerl does the same as EMBOSS - they use an "X" when the
codon could be either an amino acid OR a stop codon.

My quick BioPerl script,
================================================
use Bio::Seq
$nuc_str = 'NNNTANTARTAGTAYTAC';

print "BioPerl translation of:\n";
$seq_obj = Bio::Seq->new(-seq => $nuc_str);
print $seq_obj->seq();
print "\n\n";

print "Sequence object's translation method:\n";
print $seq_obj->translate()->seq();
print "\n\n";

use Bio::Perl;
print "translate_as_string:\n";
print translate_as_string($nuc_str);
print "\n";
================================================

And the output:
================================================
BioPerl translation of:
NNNTANTARTAGTAYTAC

Sequence object's translation method:
XX**YY

translate_as_string:
XX**YY
================================================

There does seem to be a consensus building here!


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