[Bioperl-l] Frame translation gets an extra aa?

Karger, Amir akarger at CGR.Harvard.edu
Fri Jan 14 18:06:47 UTC 2011

Apologies if this question has been asked before, or if it's so stupid that nobody was silly enough to ask it before. 

(Using Bioperl 1.6.1)

perl -l -MBio::Seq -e '$x=Bio::Seq->new(-display_id=>"foo",-seq=>"AAACCCTTTGGG"); print $x->translate(-frame=>1)->seq'

Um, why is GG being translated to G? Shouldn't you not translate if you only have 2 bp left? That is, even if you know that GGX translates to amino acid G for X in (A,C,G,T) you don't actually have that third bp right now. In real life, would an mRNA get translated even if it's missing the third base pair?

-Amir Karger
Team Lead for Scientific Applications
Research Computing, Division of Science, FAS
Harvard University

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