[Biopython-dev] [Bug 2381] translate and transcribe methods for the Seq object (in Bio.Seq)

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http://bugzilla.open-bio.org/show_bug.cgi?id=2381





------- Comment #54 from lpritc at scri.sari.ac.uk  2008-11-27 04:56 EST -------
(In reply to comment #53)
> (In reply to comment #27)
> > Created an attachment (id=1032)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1032&action=view) [details] [details]
> > Patch to Bio/Seq.py to add start codon handling to translation
> > 
> > Patch adds a new boolean argument to the translate method and function, called
> > "init" (rather than my earlier suggestions like "from_start" or "check_start"
> > which could be considered misleading).

[...]

> I don't like the "init" argument either. I would call it force_initiator_Met
> instead. BTW, non-canonical initiator codon is CUG, where did you found UUG?

This may clarify things:

>From the E. coli K-12 sequencing paper
(http://dx.doi.org/10.1126/science.277.5331.1453):

"The distribution of start codons is as follows: ATG, 3542; GTG, 612; and TTG,
130. There is also one ATT and possibly a CTG"

It's not that unusual an occurrence, and there are a small number of known
alternative start codons.  'Forcing' a Met start imposes the result that the
first codon is a methionine, rather than checking that the first codon *could
be* a methionine.  I prefer the second behaviour.

L.


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