[Bioperl-l] Re: translation using Bioperl

[Will Fischer]

On Tue, 25 Jul 2000, Heikki Lehvaslaiho wrote:
  ...  
  To summarize: The amino acid that starts a polypeptide in translation
  process is always methionin, even if an alternative initiator codon is
  used. That means that even when using the standard codon table, the
  correct translation of the sequence 'AGT TGA ...' is 'MV...'.

Errrr... How's that again?  I'm guessing you mean 'AGT GTA', but even
so, _only_ valid start codons encode the initial methionine.  A start
codon _is_ a start codon because there is a special tRNA (loaded with
a modified methionine) that matches it.

Correct behavior (IMHO) would be to check whether the first codon
matches a valid start (in the genetic code being used): if yes, 
put in Met; otherwise, put in the default amino-acid and
(perhaps) complain.  

Since (shame on me) I haven't played with the relevant modules yet,
I can't give you a modest or immodest opinion about how it should be
coded. 

 -- Will
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Will Fischer
                  
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