[Bioperl-l] Re: translation using Bioperl

Will Fischer wfischer@indiana.edu
Tue, 25 Jul 2000 13:40:44 -0500


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
____________________________________________________________
Will Fischer
                  
Biology Department                      wfischer@indiana.edu
Indiana University                      Lab:    812-855-2549
Jordan Hall 142                         FAX:    812-855-6705
1001 E. Third Street
Bloomington, IN  47405-3700 USA