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// Biopython CodonTable error?
// February 18, 2011 at 3:02 PM

http://stackoverflow.com/questions/5045967/biopython-codontable-error
Hello, I am writing some code intended to translate ambiguous DNA codes into possible amino acids and I am seeing some strange translation from the Biopython 1.56 package.  It appears to be translating ambiguous DNA codes to 'J' which does not exist as a code for anything.  I am running python 2.6.1 on Mac OS 10.6.6. 

For example:

>>>from Bio.Seq import *
>>>translate('ARAWTAGKAMTA')
'XJXJ'


or 

>>>from Bio.Seq import Seq
>>>c = Seq('ARAWTAGKAMTA')
>>>c.translate().tostring()
'XJXJ'


I have looked through the Bio.Data.CodonTable source and Bio.Seq source and I cannot find a reason why this would be happening.  Any ideas?

Thanks!

Mark


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