[Biopython-dev] [Bug 2653] Bio.SeqUtils.CodonUsage is not translation table aware

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2653


rjalves at igc.gulbenkian.pt changed:

           What    |Removed                     |Added
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                 CC|                            |rjalves at igc.gulbenkian.pt




------- Comment #1 from rjalves at igc.gulbenkian.pt  2008-11-11 13:09 EST -------
Thanks for the heads up Peter.

Also related to the reference codon table used... There is the possibility of a
codon being completely absent in all given sequences. In this case the
CodonAdaptationIndex.generate_index() function fails with a ZeroDivisionError
on line 90.

The resource at http://phenotype.biosci.umbc.edu/index.php?page=What_is_CAI
might give some good indications on how to work around this and also other
(improved?) implementations of CAI.

Obviously if you use a different SynonymousCodons table the picture may change.

Renato.


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