CODEWITHSUNDEEP
pythonbiopython
talonsensei
talonsensei

Reputation: 235

Biopython CodonTable error?

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

Upvotes: 1

Views: 547

Answers (1)

Peter Cock
Peter Cock

Reputation: 1614

J is Leucine (L) or Isoleucine (I), used in mass-spec (NMR).

See also http://biostar.stackexchange.com/questions/5688/biopython-translation-error

Upvotes: 4

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