[Bioperl-l] Re: translation using Bioperl

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Tue, 25 Jul 2000 20:49:07 +0100

used. That means that even when using the standard codon table, the
correct translation of the sequence 'AGT TGA ...' is 'MV...'.

I've fixed this in bioperl live and 06 CVS branches.

If you want to catch those cases where translation is NOT started by a
valid initiator codon, you can now set ->verbose to true in your
PrimarySeq object and it will warn you.


   What do you mean by 'catch'? 'verbose' suggests that a warning will be
   *printed*, which is not what I want when I translate EST sequences. I'm
   not sure what your change implies: does it mean that any nucleotide
   sequence will give a translation starting with Methionine? If so, there
   should be an option to turn this off, because otherwise you will be
   unable to properly (well, I know ...) translate EST sequences.